Class org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RMSMappingQualityUnitTest

all > org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific > AS_RMSMappingQualityUnitTest
39

tests
0

failures
0

ignored
0.028s

duration
100%

successful

Tests

Test Duration Result
testCombineAnnotationAgainstExpected[0]([[VC Unknown @ 20:10087820-10087822 Q264.73 of type=MIXED alleles=[CAG*, <NON_REF>, C, CAGAG] attr={AS_RAW_BaseQRankSum=[|NaN|-2.1, 1|NaN], AS_RAW_MQ=123769.00|3600.00|46800.00|0.00, AS_RAW_MQRankSum=[|NaN|0.6, 1|NaN], AS_RAW_ReadPosRankSum=[|NaN|-0.4, 1|NaN], AS_SB_TABLE=[17, 18|1, 0|8, 5|0, 0], BaseQRankSum=-2.273, DP=93, ExcessHet=3.0103, MLEAC=[0, 1, 0], MLEAF=[0.00, 0.500, 0.00], MQRankSum=0.678, RAW_MQ=329810.00, ReadPosRankSum=-0.492} GT=GT:AD:GQ:PL:SB 0/2:35,1,13,0:99:302,490,2306,0,1170,1079,483,1995,1169,1922:17,18,9,5 filters=, [VC Unknown @ 20:10087820 Q568.73 of type=MIXED alleles=[C*, <NON_REF>, CAGAG, CAGAGAG] attr={AS_RAW_BaseQRankSum=[|NaN|1.0, 1|NaN], AS_RAW_MQ=97208.00|4441.00|47258.00|0.00, AS_RAW_MQRankSum=[|NaN|-3.1, 1|NaN], AS_RAW_ReadPosRankSum=[|NaN|-0.3, 1|NaN], AS_SB_TABLE=[16, 13|0, 2|12, 12|0, 0], BaseQRankSum=0.955, DP=74, ExcessHet=3.0103, MLEAC=[0, 1, 0], MLEAF=[0.00, 0.500, 0.00], MQRankSum=-3.130, RAW_MQ=211789.00, ReadPosRankSum=-0.254} GT=GT:AD:GQ:PL:SB 0/2:29,2,24,0:99:606,627,1620,0,864,849,697,1597,927,1653:16,13,12,14 filters=], [VC Unknown @ 20:10087820-10087822 Q. of type=MIXED alleles=[CAG*, <NON_REF>, C, CAGAG, CAGAGAG, CAGAGAGAG] attr={AS_RAW_BaseQRankSum=[||1.0, 1||-2.1, 1|], AS_RAW_MQ=220977.00|4441.00|47258.00|3600.00|46800.00|0.00, AS_RAW_MQRankSum=[||-3.1, 1||0.6, 1|], AS_RAW_ReadPosRankSum=[||-0.3, 1||-0.4, 1|], AS_SB_TABLE=[33, 31|0, 2|12, 12|1, 0|8, 5|0, 0], BaseQRankSum=0.955, DP=167, ExcessHet=3.01, MQRankSum=0.678, RAW_MQ=541599.00, ReadPosRankSum=-2.540e-01} GT=GT:AD:GQ:PL:SB ./.:35,0,0,1,13,0:99:302,483,1922,483,1922,1922,490,1995,1995,2306,0,1169,1169,1170,1079,483,1922,1922,1995,1169,1922:17,18,9,5 ./.:29,2,24,0,0,0:99:606,627,1620,0,864,849,697,1597,927,1653,697,1597,927,1653,1653,697,1597,927,1653,1653,1653:16,13,12,14 filters=, [VC Unknown @ 20:10087820 Q892.52 of type=INDEL alleles=[C*, CAG, CAGAGAG] attr={AC=[1, 1], AF=[0.250, 0.250], AN=4, AS_BaseQRankSum=[1.000, -2.100], AS_FS=[0.000, 2.538], AS_MQ=[44.37, 60.00], AS_MQRankSum=[-3.100, 0.600], AS_QD=[6.80, 3.82], AS_ReadPosRankSum=[-0.300, -0.400], AS_SOR=[0.634, 1.096], BaseQRankSum=0.955, DP=167, ExcessHet=4.7712, FS=0.000, MLEAC=[1, 1], MLEAF=[0.250, 0.250], MQ=56.95, MQRankSum=0.678, QD=8.84, RAW_MQ=541599.00, ReadPosRankSum=-2.540e-01, SOR=0.728} GT=GT:AD:GQ:PL 0/2:35,0,13:99:302,483,1922,0,1169,1079 0/1:29,24,0:99:606,0,849,697,927,1653 filters=) 0.001s passed
testCombineAnnotationAgainstExpected[10]([[VC Unknown @ 20:10433575 Q1122.77 of type=MIXED alleles=[C*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|3.8, 1|NaN], AS_RAW_MQ=119641.00|100251.00|0.00, AS_RAW_MQRankSum=[|-1.2, 1|NaN], AS_RAW_ReadPosRankSum=[|0.8, 1|NaN], AS_SB_TABLE=[31, 3|26, 4|0, 0], BaseQRankSum=3.811, DP=64, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=-1.123, RAW_MQ=219892.00, ReadPosRankSum=0.830} GT=GT:AD:GQ:PGT:PID:PL:SB 0/1:34,30,0:99:0|1:10433560_C_A:1151,0,3385,1260,3476,4735:31,3,26,4 filters=, [VC Unknown @ 20:10433505-10433707 Q. of type=SYMBOLIC alleles=[T*, <NON_REF>] attr={END=10433707} GT=[[NA12892 T*/T* GQ 99 DP 51 PL 0,99,1485 {MIN_DP=39}]] filters=], [VC Unknown @ 20:10433575 Q. of type=MIXED alleles=[C*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|3.8, 1|], AS_RAW_MQ=119641.00|100251.00|0.00, AS_RAW_MQRankSum=[|-1.2, 1|], AS_RAW_ReadPosRankSum=[|0.8, 1|], AS_SB_TABLE=[31, 3|26, 4|0, 0], BaseQRankSum=3.81, DP=103, ExcessHet=3.01, MQRankSum=-1.123e+00, RAW_MQ=219892.00, ReadPosRankSum=0.830} GT=GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:SB ./.:34,30,0:.:99:.:0|1:10433560_C_A:1151,0,3385,1260,3476,4735:31,3,26,4 ./.:.:51:99:39:.:.:0,99,1485,99,1485,1485 filters=, [VC Unknown @ 20:10433575 Q1142.88 of type=SNP alleles=[C*, T] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=3.800, AS_FS=1.568, AS_MQ=57.81, AS_MQRankSum=-1.200, AS_QD=17.86, AS_ReadPosRankSum=0.800, AS_SOR=0.375, BaseQRankSum=3.81, DP=103, ExcessHet=3.0103, FS=1.568, MLEAC=1, MLEAF=0.250, MQ=58.62, MQRankSum=-1.123e+00, QD=17.86, RAW_MQ=219892.00, ReadPosRankSum=0.830, SOR=0.375} GT=GT:AD:DP:GQ:PGT:PID:PL 0/1:34,30:.:99:0|1:10433560_C_A:1151,0,3385 0/0:39,0:39:99:.:.:0,99,1485 filters=) 0.001s passed
testCombineAnnotationAgainstExpected[11]([[VC Unknown @ 20:10433594 Q1084.77 of type=MIXED alleles=[C*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|4.8, 1|NaN], AS_RAW_MQ=108841.00|85615.00|0.00, AS_RAW_MQRankSum=[|-2.4, 1|NaN], AS_RAW_ReadPosRankSum=[|-0.6, 1|NaN], AS_SB_TABLE=[28, 3|25, 4|0, 0], BaseQRankSum=4.816, DP=61, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=-2.334, RAW_MQ=195825.00, ReadPosRankSum=-0.502} GT=GT:AD:GQ:PGT:PID:PL:SB 0/1:31,29,0:99:0|1:10433560_C_A:1113,0,3070,1206,3160,4366:28,3,25,4 filters=, [VC Unknown @ 20:10433505-10433707 Q. of type=SYMBOLIC alleles=[T*, <NON_REF>] attr={END=10433707} GT=[[NA12892 T*/T* GQ 99 DP 51 PL 0,99,1485 {MIN_DP=39}]] filters=], [VC Unknown @ 20:10433594 Q. of type=MIXED alleles=[C*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|4.8, 1|], AS_RAW_MQ=108841.00|85615.00|0.00, AS_RAW_MQRankSum=[|-2.4, 1|], AS_RAW_ReadPosRankSum=[|-0.6, 1|], AS_SB_TABLE=[28, 3|25, 4|0, 0], BaseQRankSum=4.82, DP=100, ExcessHet=3.01, MQRankSum=-2.334e+00, RAW_MQ=195825.00, ReadPosRankSum=-5.020e-01} GT=GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:SB ./.:31,29,0:.:99:.:0|1:10433560_C_A:1113,0,3070,1206,3160,4366:28,3,25,4 ./.:.:51:99:39:.:.:0,99,1485,99,1485,1485 filters=, [VC Unknown @ 20:10433594 Q1104.88 of type=SNP alleles=[C*, T] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=4.800, AS_FS=1.535, AS_MQ=54.33, AS_MQRankSum=-2.400, AS_QD=18.42, AS_ReadPosRankSum=-0.600, AS_SOR=0.415, BaseQRankSum=4.82, DP=100, ExcessHet=3.0103, FS=1.535, MLEAC=1, MLEAF=0.250, MQ=56.66, MQRankSum=-2.334e+00, QD=18.41, RAW_MQ=195825.00, ReadPosRankSum=-5.020e-01, SOR=0.415} GT=GT:AD:DP:GQ:PGT:PID:PL 0/1:31,29:.:99:0|1:10433560_C_A:1113,0,3070 0/0:39,0:39:99:.:.:0,99,1485 filters=) 0s passed
testCombineAnnotationAgainstExpected[12]([[VC Unknown @ 20:10433955 Q997.73 of type=MIXED alleles=[C*, <NON_REF>, CGTGTGTGTGTAT] attr={AS_RAW_BaseQRankSum=[|0.4, 1|NaN], AS_RAW_MQ=59810.00|39497.00|0.00, AS_RAW_MQRankSum=[|-4.0, 1|NaN], AS_RAW_ReadPosRankSum=[|-0.8, 1|NaN], AS_SB_TABLE=[12, 6|16, 8|0, 0], BaseQRankSum=0.422, DP=47, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=-4.001, RAW_MQ=117307.00, ReadPosRankSum=-0.789} GT=GT:AD:GQ:PL:SB 0/1:18,24,0:99:1035,0,1217,1090,1298,2389:12,6,16,8 filters=, [VC Unknown @ 20:10433722-10433955 Q. of type=SYMBOLIC alleles=[A*, <NON_REF>] attr={END=10433955} GT=GT:DP:GQ:MIN_DP:PL 0/0:59:99:37:0,99,1485 filters=], [VC Unknown @ 20:10433955 Q. of type=MIXED alleles=[C*, <NON_REF>, CGTGTGTGTGTAT] attr={AS_RAW_BaseQRankSum=[|0.4, 1|], AS_RAW_MQ=59810.00|39497.00|0.00, AS_RAW_MQRankSum=[|-4.0, 1|], AS_RAW_ReadPosRankSum=[|-0.8, 1|], AS_SB_TABLE=[12, 6|16, 8|0, 0], BaseQRankSum=0.422, DP=84, ExcessHet=3.01, MQRankSum=-4.001e+00, RAW_MQ=117307.00, ReadPosRankSum=-7.890e-01} GT=GT:AD:DP:GQ:MIN_DP:PL:SB ./.:18,24,0:.:99:.:1035,0,1217,1090,1298,2389:12,6,16,8 ./.:.:59:99:37:0,99,1485,99,1485,1485 filters=, [VC Unknown @ 20:10433955 Q1026.91 of type=INDEL alleles=[C*, CGTGTGTGTGTAT] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=0.400, AS_FS=0.000, AS_MQ=40.57, AS_MQRankSum=-4.000, AS_QD=24.45, AS_ReadPosRankSum=-0.800, AS_SOR=0.710, BaseQRankSum=0.422, DP=84, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.250, MQ=49.96, MQRankSum=-4.001e+00, QD=24.45, RAW_MQ=117307.00, ReadPosRankSum=-7.890e-01, SOR=0.710} GT=GT:AD:DP:GQ:PL 0/1:18,24:.:99:1035,0,1217 0/0:37,0:37:99:0,99,1485 filters=) 0.001s passed
testCombineAnnotationAgainstExpected[13]([[VC Unknown @ 20:10434177 Q1446.77 of type=MIXED alleles=[A*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|0.9, 1|NaN], AS_RAW_MQ=108000.00|133784.00|0.00, AS_RAW_MQRankSum=[|-2.5, 1|NaN], AS_RAW_ReadPosRankSum=[|-0.9, 1|NaN], AS_SB_TABLE=[15, 15|23, 20|0, 0], BaseQRankSum=0.903, DP=74, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=-2.473, RAW_MQ=245384.00, ReadPosRankSum=-0.891} GT=GT:AD:GQ:PL:SB 0/1:30,43,0:99:1475,0,936,1565,1066,2631:15,15,23,20 filters=, [VC Unknown @ 20:10434083-10436207 Q. of type=SYMBOLIC alleles=[G*, <NON_REF>] attr={END=10436207} GT=GT:DP:GQ:MIN_DP:PL 0/0:75:99:37:0,102,1530 filters=], [VC Unknown @ 20:10434177 Q. of type=MIXED alleles=[A*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|0.9, 1|], AS_RAW_MQ=108000.00|133784.00|0.00, AS_RAW_MQRankSum=[|-2.5, 1|], AS_RAW_ReadPosRankSum=[|-0.9, 1|], AS_SB_TABLE=[15, 15|23, 20|0, 0], BaseQRankSum=0.903, DP=111, ExcessHet=3.01, MQRankSum=-2.473e+00, RAW_MQ=245384.00, ReadPosRankSum=-8.910e-01} GT=GT:AD:DP:GQ:MIN_DP:PL:SB ./.:30,43,0:.:99:.:1475,0,936,1565,1066,2631:15,15,23,20 ./.:.:75:99:37:0,102,1530,102,1530,1530 filters=, [VC Unknown @ 20:10434177 Q1466.88 of type=SNP alleles=[A*, T] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=0.900, AS_FS=0.888, AS_MQ=55.78, AS_MQRankSum=-2.500, AS_QD=20.10, AS_ReadPosRankSum=-0.900, AS_SOR=0.836, BaseQRankSum=0.903, DP=111, ExcessHet=3.0103, FS=0.888, MLEAC=1, MLEAF=0.250, MQ=57.58, MQRankSum=-2.473e+00, QD=20.09, RAW_MQ=245384.00, ReadPosRankSum=-8.910e-01, SOR=0.836} GT=GT:AD:DP:GQ:PL 0/1:30,43:.:99:1475,0,936 0/0:37,0:37:99:0,102,1530 filters=) 0.001s passed
testCombineAnnotationAgainstExpected[14]([[VC Unknown @ 20:10434384-10434385 Q752.73 of type=MIXED alleles=[TA*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|-0.1, 1|NaN], AS_RAW_MQ=123769.00|118800.00|0.00, AS_RAW_MQRankSum=[|1.0, 1|NaN], AS_RAW_ReadPosRankSum=[|0.4, 1|NaN], AS_SB_TABLE=[22, 13|21, 12|0, 0], BaseQRankSum=-0.100, DP=71, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=1.000, RAW_MQ=253369.00, ReadPosRankSum=0.497} GT=GT:AD:GQ:PL:SB 0/1:35,33,0:99:790,0,846,895,945,1840:22,13,21,12 filters=, [VC Unknown @ 20:10434083-10436207 Q. of type=SYMBOLIC alleles=[G*, <NON_REF>] attr={END=10436207} GT=GT:DP:GQ:MIN_DP:PL 0/0:75:99:37:0,102,1530 filters=], [VC Unknown @ 20:10434384-10434385 Q. of type=MIXED alleles=[TA*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|-0.1, 1|], AS_RAW_MQ=123769.00|118800.00|0.00, AS_RAW_MQRankSum=[|1.0, 1|], AS_RAW_ReadPosRankSum=[|0.4, 1|], AS_SB_TABLE=[22, 13|21, 12|0, 0], BaseQRankSum=-1.000e-01, DP=108, ExcessHet=3.01, MQRankSum=1.00, RAW_MQ=253369.00, ReadPosRankSum=0.497} GT=GT:AD:DP:GQ:MIN_DP:PL:SB ./.:35,33,0:.:99:.:790,0,846,895,945,1840:22,13,21,12 ./.:.:75:99:37:0,102,1530,102,1530,1530 filters=, [VC Unknown @ 20:10434384-10434385 Q781.88 of type=INDEL alleles=[TA*, T] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=-0.100, AS_FS=0.000, AS_MQ=60.00, AS_MQRankSum=1.000, AS_QD=11.50, AS_ReadPosRankSum=0.400, AS_SOR=0.723, BaseQRankSum=-1.000e-01, DP=108, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.250, MQ=59.74, MQRankSum=1.00, QD=11.50, RAW_MQ=253369.00, ReadPosRankSum=0.497, SOR=0.723} GT=GT:AD:DP:GQ:PL 0/1:35,33:.:99:790,0,846 0/0:37,0:37:99:0,102,1530 filters=) 0s passed
testCombineAnnotationAgainstExpected[15]([[VC Unknown @ 20:10435067-10435069 Q1416.73 of type=MIXED alleles=[GTA*, <NON_REF>, G] attr={AS_RAW_BaseQRankSum=[|2.6, 1|NaN], AS_RAW_MQ=108000.00|133200.00|0.00, AS_RAW_MQRankSum=[|0.0, 1|NaN], AS_RAW_ReadPosRankSum=[|-0.2, 1|NaN], AS_SB_TABLE=[15, 15|22, 15|0, 0], BaseQRankSum=2.601, DP=67, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=0.000, RAW_MQ=241200.00, ReadPosRankSum=-0.183} GT=GT:AD:GQ:PL:SB 0/1:30,37,0:99:1454,0,1191,1544,1303,2847:15,15,22,15 filters=, [VC Unknown @ 20:10434083-10436207 Q. of type=SYMBOLIC alleles=[G*, <NON_REF>] attr={END=10436207} GT=[[NA12892 G*/G* GQ 99 DP 75 PL 0,102,1530 {MIN_DP=37}]] filters=], [VC Unknown @ 20:10435067-10435069 Q. of type=MIXED alleles=[GTA*, <NON_REF>, G] attr={AS_RAW_BaseQRankSum=[|2.6, 1|], AS_RAW_MQ=108000.00|133200.00|0.00, AS_RAW_MQRankSum=[|0.0, 1|], AS_RAW_ReadPosRankSum=[|-0.2, 1|], AS_SB_TABLE=[15, 15|22, 15|0, 0], BaseQRankSum=2.60, DP=104, ExcessHet=3.01, MQRankSum=0.00, RAW_MQ=241200.00, ReadPosRankSum=-1.830e-01} GT=GT:AD:DP:GQ:MIN_DP:PL:SB ./.:30,37,0:.:99:.:1454,0,1191,1544,1303,2847:15,15,22,15 ./.:.:75:99:37:0,102,1530,102,1530,1530 filters=, [VC Unknown @ 20:10435067-10435069 Q1445.88 of type=INDEL alleles=[GTA*, G] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=2.600, AS_FS=3.289, AS_MQ=60.00, AS_MQRankSum=0.000, AS_QD=21.58, AS_ReadPosRankSum=-0.200, AS_SOR=1.121, BaseQRankSum=2.60, DP=104, ExcessHet=3.0103, FS=3.289, MLEAC=1, MLEAF=0.250, MQ=60.00, MQRankSum=0.00, QD=21.58, RAW_MQ=241200.00, ReadPosRankSum=-1.830e-01, SOR=1.121} GT=GT:AD:DP:GQ:PL 0/1:30,37:.:99:1454,0,1191 0/0:37,0:37:99:0,102,1530 filters=) 0.001s passed
testCombineAnnotationAgainstExpected[16]([[VC Unknown @ 20:10434258 Q1214.77 of type=MIXED alleles=[G*, <NON_REF>, A] attr={AS_RAW_BaseQRankSum=[|3.0, 1|NaN], AS_RAW_MQ=109369.00|106451.00|0.00, AS_RAW_MQRankSum=[|-2.9, 1|NaN], AS_RAW_ReadPosRankSum=[|-0.2, 1|NaN], AS_SB_TABLE=[19, 12|24, 14|0, 0], BaseQRankSum=3.063, DP=70, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=-2.871, RAW_MQ=219420.00, ReadPosRankSum=-0.155} GT=GT:AD:GQ:PL:SB 0/1:31,38,0:99:1243,0,1003,1337,1118,2455:19,12,24,14 filters=, [VC Unknown @ 20:10434083-10436207 Q. of type=SYMBOLIC alleles=[G*, <NON_REF>] attr={END=10436207} GT=GT:DP:GQ:MIN_DP:PL 0/0:75:99:37:0,102,1530 filters=], [VC Unknown @ 20:10434258 Q. of type=MIXED alleles=[G*, <NON_REF>, A] attr={AS_RAW_BaseQRankSum=[|3.0, 1|], AS_RAW_MQ=109369.00|106451.00|0.00, AS_RAW_MQRankSum=[|-2.9, 1|], AS_RAW_ReadPosRankSum=[|-0.2, 1|], AS_SB_TABLE=[19, 12|24, 14|0, 0], BaseQRankSum=3.06, DP=107, ExcessHet=3.01, MQRankSum=-2.871e+00, RAW_MQ=219420.00, ReadPosRankSum=-1.550e-01} GT=GT:AD:DP:GQ:MIN_DP:PL:SB ./.:31,38,0:.:99:.:1243,0,1003,1337,1118,2455:19,12,24,14 ./.:.:75:99:37:0,102,1530,102,1530,1530 filters=, [VC Unknown @ 20:10434258 Q1234.88 of type=SNP alleles=[G*, A] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=3.000, AS_FS=0.000, AS_MQ=52.93, AS_MQRankSum=-2.900, AS_QD=17.90, AS_ReadPosRankSum=-0.200, AS_SOR=0.776, BaseQRankSum=3.06, DP=107, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.250, MQ=55.99, MQRankSum=-2.871e+00, QD=17.90, RAW_MQ=219420.00, ReadPosRankSum=-1.550e-01, SOR=0.776} GT=GT:AD:DP:GQ:PL 0/1:31,38:.:99:1243,0,1003 0/0:37,0:37:99:0,102,1530 filters=) 0.001s passed
testCombineAnnotationAgainstExpected[17]([[VC Unknown @ 20:10436227-10436247 Q1187.73 of type=MIXED alleles=[TTTTATTTATTTATTTATTTA*, <NON_REF>, T, TTTTATTTATTTATTTATTTATTTA] attr={AS_RAW_BaseQRankSum=|||, AS_RAW_MQ=3600.00|25702.00|19682.00|0.00, AS_RAW_MQRankSum=|||, AS_RAW_ReadPosRankSum=|||, AS_SB_TABLE=[1, 0|14, 10|4, 3|0, 0], BaseQRankSum=-1.450, DP=75, ExcessHet=3.0103, MLEAC=[1, 1, 0], MLEAF=[0.500, 0.500, 0.00], MQRankSum=-1.660, RAW_MQ=201025.00, ReadPosRankSum=1.303} GT=GT:AD:GQ:PL:SB 1/2:1,24,7,0:99:1225,241,589,947,0,970,1258,491,1017,1480:1,0,18,13 filters=, [VC Unknown @ 20:10436227 Q387.74 of type=MIXED alleles=[T*, <NON_REF>, TTTTA] attr={AS_RAW_BaseQRankSum=||, AS_RAW_MQ=0.00|29194.00|0.00, AS_RAW_MQRankSum=||, AS_RAW_ReadPosRankSum=||, AS_SB_TABLE=[0, 0|7, 3|0, 0], DP=33, ExcessHet=3.0103, MLEAC=[2, 0], MLEAF=[1.00, 0.00], RAW_MQ=111994.00} GT=GT:AD:GQ:PL:SB 1/1:0,10,0:29:425,29,0,427,30,428:0,0,7,3 filters=], [VC Unknown @ 20:10436227-10436247 Q. of type=MIXED alleles=[TTTTATTTATTTATTTATTTA*, <NON_REF>, T, TTTTATTTATTTATTTATTTATTTA] attr={AS_RAW_BaseQRankSum=|||, AS_RAW_MQ=3600.00|48876.00|25702.00|0.00, AS_RAW_MQRankSum=|||, AS_RAW_ReadPosRankSum=|||, AS_SB_TABLE=[1, 0|11, 6|14, 10|0, 0], BaseQRankSum=-1.450e+00, DP=108, ExcessHet=3.01, MQRankSum=-1.660e+00, RAW_MQ=313019.00, ReadPosRankSum=1.30} GT=GT:AD:GQ:PL:SB ./.:1,7,24,0:99:1225,947,970,241,0,589,1258,1017,491,1480:1,0,18,13 ./.:0,10,0,0:29:425,29,0,427,30,428,427,30,428,428:0,0,7,3 filters=, [VC Unknown @ 20:10436227-10436247 Q1627.36 of type=INDEL alleles=[TTTTATTTATTTATTTATTTA*, T, TTTTATTTATTTATTTATTTATTTA] attr={AC=[3, 1], AF=[0.750, 0.250], AN=4, AS_BaseQRankSum=[., .], AS_FS=[0.000, 0.000], AS_MQ=[53.62, 32.72], AS_MQRankSum=[., .], AS_QD=[27.24, 28.20], AS_ReadPosRankSum=[., .], AS_SOR=[0.551, 0.382], BaseQRankSum=-1.450e+00, DP=108, ExcessHet=3.0103, FS=0.000, MLEAC=[3, 1], MLEAF=[0.750, 0.250], MQ=53.84, MQRankSum=-1.660e+00, QD=25.00, RAW_MQ=313019.00, ReadPosRankSum=1.30, SOR=0.460} GT=GT:AD:GQ:PL 1/2:1,7,24:99:1225,947,970,241,0,589 1/1:0,10,0:29:425,29,0,427,30,428 filters=) 0s passed
testCombineAnnotationAgainstExpected[18]([[VC Unknown @ 20:10684106-10684118 Q0.00 of type=MIXED alleles=[CCTTTCTTTCTTT*, <NON_REF>, C, CCTTTCTTT] attr={AS_RAW_BaseQRankSum=|NaN|NaN|NaN, AS_RAW_MQ=101641.00|0.00|0.00|0.00, AS_RAW_MQRankSum=|NaN|NaN|NaN, AS_RAW_ReadPosRankSum=|NaN|NaN|NaN, AS_SB_TABLE=[9, 20|0, 0|0, 0|0, 0], DP=60, ExcessHet=3.0103, MLEAC=[0, 0, 0], MLEAF=[0.00, 0.00, 0.00], RAW_MQ=196687.00} GT=GT:AD:GQ:PL:SB 0/0:29,0,0,0:84:0,101,3282,84,1698,1592,112,2553,1707,2450:9,20,0,0 filters=, [VC Unknown @ 20:10684106 Q. of type=SYMBOLIC alleles=[C*, <NON_REF>] attr={END=10684106} GT=GT:DP:GQ:MIN_DP:PL 0/0:46:99:46:0,108,1620 filters=], [VC Unknown @ 20:10684106-10684118 Q. of type=MIXED alleles=[CCTTTCTTTCTTT*, <NON_REF>, C, CCTTTCTTT] attr={AS_RAW_BaseQRankSum=|||, AS_RAW_MQ=101641.00|0.00|0.00|0.00, AS_RAW_MQRankSum=|||, AS_RAW_ReadPosRankSum=|||, AS_SB_TABLE=[9, 20|0, 0|0, 0|0, 0], DP=106, ExcessHet=3.01, RAW_MQ=196687.00} GT=GT:AD:DP:GQ:MIN_DP:PL:SB ./.:29,0,0,0:.:84:.:0,101,3282,84,1698,1592,112,2553,1707,2450:9,20,0,0 ./.:.:46:99:46:0,108,1620,108,1620,1620,108,1620,1620,1620 filters=, null) 0.001s passed
testCombineAnnotationAgainstExpected[1]([[VC Unknown @ 20:10433312-10433319 Q0.00 of type=MIXED alleles=[CAAAAAAA*, <NON_REF>, C, CAAAAAA] attr={AS_RAW_BaseQRankSum=|NaN|NaN|NaN, AS_RAW_MQ=29659.00|0.00|0.00|0.00, AS_RAW_MQRankSum=|NaN|NaN|NaN, AS_RAW_ReadPosRankSum=|NaN|NaN|NaN, AS_SB_TABLE=[6, 10|0, 0|0, 0|0, 0], DP=37, ExcessHet=3.0103, MLEAC=[0, 0, 0], MLEAF=[0.00, 0.00, 0.00], RAW_MQ=83187.00} GT=GT:AD:GQ:PL:SB 0/0:16,0,0,0:48:0,74,1123,48,615,553,75,891,606,839:6,10,0,0 filters=, [VC Unknown @ 20:10433312-10433319 Q0.00 of type=MIXED alleles=[CAAAAAAA*, <NON_REF>, C, CAAAAAA] attr={AS_RAW_BaseQRankSum=|NaN|NaN|NaN, AS_RAW_MQ=46939.00|0.00|1682.00|0.00, AS_RAW_MQRankSum=|NaN|NaN|NaN, AS_RAW_ReadPosRankSum=|NaN|NaN|NaN, AS_SB_TABLE=[13, 10|0, 0|1, 1|0, 0], BaseQRankSum=1.588, DP=43, ExcessHet=3.0103, MLEAC=[0, 0, 0], MLEAF=[0.00, 0.00, 0.00], MQRankSum=-1.259, RAW_MQ=95936.00, ReadPosRankSum=0.333} GT=GT:AD:GQ:PL:SB 0/0:23,0,2,0:10:0,81,1139,10,811,747,81,1026,798,979:13,10,1,1 filters=], [VC Unknown @ 20:10433312-10433319 Q. of type=MIXED alleles=[CAAAAAAA*, <NON_REF>, C, CAAAAAA] attr={AS_RAW_BaseQRankSum=|||, AS_RAW_MQ=76598.00|0.00|1682.00|0.00, AS_RAW_MQRankSum=|||, AS_RAW_ReadPosRankSum=|||, AS_SB_TABLE=[19, 20|0, 0|1, 1|0, 0], BaseQRankSum=1.59, DP=80, ExcessHet=3.01, MQRankSum=-1.259e+00, RAW_MQ=179123.00, ReadPosRankSum=0.333} GT=GT:AD:GQ:PL:SB ./.:16,0,0,0:48:0,74,1123,48,615,553,75,891,606,839:6,10,0,0 ./.:23,0,2,0:10:0,81,1139,10,811,747,81,1026,798,979:13,10,1,1 filters=, null) 0.001s passed
testCombineAnnotationAgainstExpected[2]([[VC Unknown @ 20:10433322 Q86.73 of type=MIXED alleles=[A*, <NON_REF>, AT] attr={AS_RAW_BaseQRankSum=[|2.5, 1|NaN], AS_RAW_MQ=14418.00|9723.00|0.00, AS_RAW_MQRankSum=[|1.1, 1|NaN], AS_RAW_ReadPosRankSum=[|2.0, 1|NaN], AS_SB_TABLE=[5, 6|2, 3|0, 0], BaseQRankSum=2.564, DP=35, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=1.122, RAW_MQ=67710.00, ReadPosRankSum=2.044} GT=GT:AD:GQ:PL:SB 0/1:11,5,0:99:124,0,369,158,384,542:5,6,2,3 filters=, [VC Unknown @ 20:10433322 Q412.79 of type=MIXED alleles=[A*, <NON_REF>, AT, ATAT] attr={AS_RAW_BaseQRankSum=[|0.8, 1|NaN|NaN], AS_RAW_MQ=3364.00|31589.00|2523.00|0.00, AS_RAW_MQRankSum=[|2.2, 1|NaN|NaN], AS_RAW_ReadPosRankSum=[|1.9, 1|NaN|NaN], AS_SB_TABLE=[2, 2|6, 6|2, 1|0, 0], BaseQRankSum=0.877, DP=42, ExcessHet=3.0103, MLEAC=[1, 0, 0], MLEAF=[0.500, 0.00, 0.00], MQRankSum=1.895, RAW_MQ=86818.00, ReadPosRankSum=1.704} GT=GT:AD:GQ:PL:SB 0/1:4,12,3,0:19:450,0,46,298,19,576,442,117,506,617:2,2,8,7 filters=], [VC Unknown @ 20:10433322 Q. of type=MIXED alleles=[A*, <NON_REF>, AT, ATAT] attr={AS_RAW_BaseQRankSum=[|0.8, 1, 2.5, 1||], AS_RAW_MQ=17782.00|41312.00|2523.00|0.00, AS_RAW_MQRankSum=[|1.1, 1, 2.2, 1||], AS_RAW_ReadPosRankSum=[|1.9, 1, 2.0, 1||], AS_SB_TABLE=[7, 8|8, 9|2, 1|0, 0], BaseQRankSum=2.56, DP=77, ExcessHet=3.01, MQRankSum=1.90, RAW_MQ=154528.00, ReadPosRankSum=2.04} GT=GT:AD:GQ:PL:SB ./.:11,5,0,0:99:124,0,369,158,384,542,158,384,542,542:5,6,2,3 ./.:4,12,3,0:19:450,0,46,298,19,576,442,117,506,617:2,2,8,7 filters=, [VC Unknown @ 20:10433322 Q564.50 of type=INDEL alleles=[A*, AT] attr={AC=2, AF=0.500, AN=4, AS_BaseQRankSum=1.650, AS_FS=0.000, AS_MQ=49.30, AS_MQRankSum=1.650, AS_QD=13.75, AS_ReadPosRankSum=1.950, AS_SOR=0.681, BaseQRankSum=2.56, DP=77, ExcessHet=4.7712, FS=0.000, MLEAC=2, MLEAF=0.500, MQ=44.80, MQRankSum=1.90, QD=17.64, RAW_MQ=154528.00, ReadPosRankSum=2.04, SOR=0.582} GT=GT:AD:GQ:PL 0/1:11,5:99:124,0,369 0/1:4,12:46:450,0,46 filters=) 0.001s passed
testCombineAnnotationAgainstExpected[3]([[VC Unknown @ 20:10433324 Q199.77 of type=MIXED alleles=[A*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|2.2, 1|NaN], AS_RAW_MQ=11895.00|10564.00|0.00, AS_RAW_MQRankSum=[|0.5, 1|NaN], AS_RAW_ReadPosRankSum=[|1.5, 1|NaN], AS_SB_TABLE=[2, 6|2, 4|0, 0], BaseQRankSum=2.279, DP=33, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=0.584, RAW_MQ=60510.00, ReadPosRankSum=1.543} GT=GT:AD:GQ:PGT:PID:PL:SB 0/1:8,6,0:99:0|1:10433324_A_T:228,0,275,252,294,546:2,6,2,4 filters=, [VC Unknown @ 20:10433324 Q848.77 of type=MIXED alleles=[A*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=||, AS_RAW_MQ=841.00|38317.00|0.00, AS_RAW_MQRankSum=||, AS_RAW_ReadPosRankSum=||, AS_SB_TABLE=[0, 1|11, 9|0, 0], BaseQRankSum=1.458, DP=40, ExcessHet=3.0103, MLEAC=[2, 0], MLEAF=[1.00, 0.00], MQRankSum=0.871, RAW_MQ=79618.00, ReadPosRankSum=1.736} GT=GT:AD:GQ:PGT:PID:PL:SB 1/1:1,20,0:53:0|1:10433324_A_T:877,53,0,880,61,888:0,1,11,9 filters=], [VC Unknown @ 20:10433324 Q. of type=MIXED alleles=[A*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|2.2, 1|], AS_RAW_MQ=12736.00|48881.00|0.00, AS_RAW_MQRankSum=[|0.5, 1|], AS_RAW_ReadPosRankSum=[|1.5, 1|], AS_SB_TABLE=[2, 7|13, 13|0, 0], BaseQRankSum=2.28, DP=73, ExcessHet=3.01, MQRankSum=0.871, RAW_MQ=140128.00, ReadPosRankSum=1.74} GT=GT:AD:GQ:PGT:PID:PL:SB ./.:8,6,0:99:0|1:10433324_A_T:228,0,275,252,294,546:2,6,2,4 ./.:1,20,0:53:0|1:10433324_A_T:877,53,0,880,61,888:0,1,11,9 filters=, [VC Unknown @ 20:10433324 Q1091.09 of type=SNP alleles=[A*, T] attr={AC=3, AF=0.750, AN=4, AS_BaseQRankSum=2.200, AS_FS=6.118, AS_MQ=43.36, AS_MQRankSum=0.500, AS_QD=31.17, AS_ReadPosRankSum=1.500, AS_SOR=0.132, BaseQRankSum=2.28, DP=73, ExcessHet=3.0103, FS=6.118, MLEAC=3, MLEAF=0.750, MQ=43.81, MQRankSum=0.871, QD=31.17, RAW_MQ=140128.00, ReadPosRankSum=1.74, SOR=0.132} GT=GT:AD:GQ:PGT:PID:PL 0/1:8,6:99:0|1:10433324_A_T:228,0,275 1/1:1,20:53:1|1:10433324_A_T:877,53,0 filters=) 0.001s passed
testCombineAnnotationAgainstExpected[4]([[VC Unknown @ 20:10433326 Q199.77 of type=MIXED alleles=[A*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|0.8, 1|NaN], AS_RAW_MQ=11895.00|10564.00|0.00, AS_RAW_MQRankSum=[|0.5, 1|NaN], AS_RAW_ReadPosRankSum=[|1.4, 1|NaN], AS_SB_TABLE=[2, 6|2, 4|0, 0], BaseQRankSum=0.874, DP=31, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=0.584, RAW_MQ=53310.00, ReadPosRankSum=1.403} GT=GT:AD:GQ:PGT:PID:PL:SB 0/1:8,6,0:99:0|1:10433324_A_T:228,0,275,252,293,546:2,6,2,4 filters=, [VC Unknown @ 20:10433326 Q848.77 of type=MIXED alleles=[A*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=||, AS_RAW_MQ=841.00|38317.00|0.00, AS_RAW_MQRankSum=||, AS_RAW_ReadPosRankSum=||, AS_SB_TABLE=[0, 1|11, 9|0, 0], BaseQRankSum=1.537, DP=36, ExcessHet=3.0103, MLEAC=[2, 0], MLEAF=[1.00, 0.00], MQRankSum=0.871, RAW_MQ=65218.00, ReadPosRankSum=1.736} GT=GT:AD:GQ:PGT:PID:PL:SB 1/1:1,20,0:53:0|1:10433324_A_T:877,53,0,881,61,888:0,1,11,9 filters=], [VC Unknown @ 20:10433326 Q. of type=MIXED alleles=[A*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|0.8, 1|], AS_RAW_MQ=12736.00|48881.00|0.00, AS_RAW_MQRankSum=[|0.5, 1|], AS_RAW_ReadPosRankSum=[|1.4, 1|], AS_SB_TABLE=[2, 7|13, 13|0, 0], BaseQRankSum=1.54, DP=67, ExcessHet=3.01, MQRankSum=0.871, RAW_MQ=118528.00, ReadPosRankSum=1.74} GT=GT:AD:GQ:PGT:PID:PL:SB ./.:8,6,0:99:0|1:10433324_A_T:228,0,275,252,293,546:2,6,2,4 ./.:1,20,0:53:0|1:10433324_A_T:877,53,0,881,61,888:0,1,11,9 filters=, [VC Unknown @ 20:10433326 Q1091.09 of type=SNP alleles=[A*, T] attr={AC=3, AF=0.750, AN=4, AS_BaseQRankSum=0.800, AS_FS=6.118, AS_MQ=43.36, AS_MQRankSum=0.500, AS_QD=31.17, AS_ReadPosRankSum=1.400, AS_SOR=0.132, BaseQRankSum=1.54, DP=67, ExcessHet=3.0103, FS=6.118, MLEAC=3, MLEAF=0.750, MQ=42.06, MQRankSum=0.871, QD=31.17, RAW_MQ=118528.00, ReadPosRankSum=1.74, SOR=0.132} GT=GT:AD:GQ:PGT:PID:PL 0/1:8,6:99:0|1:10433324_A_T:228,0,275 1/1:1,20:53:1|1:10433324_A_T:877,53,0 filters=) 0s passed
testCombineAnnotationAgainstExpected[5]([[VC Unknown @ 20:10433328 Q881.73 of type=MIXED alleles=[A*, <NON_REF>, AATATAT, AATATATAT, ATATAT, ATATATAT, T] attr={AS_RAW_BaseQRankSum=||||||, AS_RAW_MQ=0.00|10564.00|2523.00|0.00|0.00|0.00|0.00, AS_RAW_MQRankSum=||||||, AS_RAW_ReadPosRankSum=||||||, AS_SB_TABLE=[0, 0|2, 4|1, 2|0, 0|0, 0|0, 0|0, 0], DP=30, ExcessHet=3.0103, MLEAC=[1, 1, 0, 0, 0, 0], MLEAF=[0.500, 0.500, 0.00, 0.00, 0.00, 0.00], RAW_MQ=49710.00} GT=GT:AD:GQ:PL:SB 1/2:0,6,3,0,0,0,0:91:919,177,246,420,0,500,470,91,514,592,483,122,379,428,563,513,192,384,470,576,640,676,211,530,616,595,658,804:0,0,3,6 filters=, [VC Unknown @ 20:10433328 Q1153.73 of type=MIXED alleles=[A*, <NON_REF>, AATATAT, AATATATAT, AATATATATAT, T] attr={AS_RAW_BaseQRankSum=|||||, AS_RAW_MQ=0.00|38317.00|0.00|0.00|0.00|0.00, AS_RAW_MQRankSum=|||||, AS_RAW_ReadPosRankSum=|||||, AS_SB_TABLE=[0, 0|11, 9|0, 0|0, 0|0, 0|0, 0], DP=36, ExcessHet=3.0103, MLEAC=[2, 0, 0, 0, 0], MLEAF=[1.00, 0.00, 0.00, 0.00, 0.00], RAW_MQ=65218.00} GT=GT:AD:GQ:PL:SB 1/1:0,20,0,0,0,0:74:1191,74,0,1085,90,1328,951,76,1182,1193,1147,93,1334,1214,1394,1132,93,1334,1213,1381,1376:0,0,11,9 filters=], [VC Unknown @ 20:10433328 Q. of type=MIXED alleles=[A*, <NON_REF>, AATATAT, AATATATAT, AATATATATAT, ATATAT, ATATATAT, T] attr={AS_RAW_BaseQRankSum=|||||||, AS_RAW_MQ=0.00|48881.00|0.00|0.00|0.00|2523.00|0.00|0.00, AS_RAW_MQRankSum=|||||||, AS_RAW_ReadPosRankSum=|||||||, AS_SB_TABLE=[0, 0|13, 13|0, 0|0, 0|0, 0|1, 2|0, 0|0, 0], DP=66, ExcessHet=3.01, RAW_MQ=114928.00} GT=GT:AD:GQ:PL:SB ./.:0,6,0,0,0,3,0,0:91:919,177,246,470,91,592,513,192,470,640,676,211,616,658,804,420,0,514,384,530,500,483,122,428,576,595,379,563,676,211,616,658,804,530,595,804:0,0,3,6 ./.:0,20,0,0,0,0,0,0:74:1191,74,0,1085,90,1328,951,76,1182,1193,1147,93,1334,1214,1394,1132,93,1334,1213,1381,1376,1132,93,1334,1213,1381,1376,1376,1132,93,1334,1213,1381,1376,1376,1376:0,0,11,9 filters=, [VC Unknown @ 20:10433328 Q2087.37 of type=MIXED alleles=[A*, ATATAT, T] attr={AC=[3, 1], AF=[0.750, 0.250], AN=4, AS_BaseQRankSum=[., .], AS_FS=[0.000, 0.000], AS_MQ=[43.36, 29.00], AS_MQRankSum=[., .], AS_QD=[25.36, 28.73], AS_ReadPosRankSum=[., .], AS_SOR=[0.693, 1.179], DP=66, ExcessHet=3.0103, FS=0.000, MLEAC=[3, 1], MLEAF=[0.750, 0.250], MQ=41.73, QD=30.97, RAW_MQ=114928.00, SOR=0.760} GT=GT:AD:GQ:PL 1/2:0,6,3:99:919,177,246,420,0,500 1/1:0,20,0:74:1191,74,0,1132,93,1376 filters=) 0.001s passed
testCombineAnnotationAgainstExpected[6]([[VC Unknown @ 20:10433382 Q603.77 of type=MIXED alleles=[T*, <NON_REF>, C] attr={AS_RAW_BaseQRankSum=[|-1.9, 1|NaN], AS_RAW_MQ=40862.00|45723.00|0.00, AS_RAW_MQRankSum=[|1.0, 1|NaN], AS_RAW_ReadPosRankSum=[|0.2, 1|NaN], AS_SB_TABLE=[10, 5|11, 4|0, 0], BaseQRankSum=-1.821, DP=30, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=1.033, RAW_MQ=86585.00, ReadPosRankSum=0.249} GT=GT:AD:GQ:PGT:PID:PL:SB 0/1:15,15,0:99:0|1:10433382_T_C:632,0,601,680,652,1332:10,5,11,4 filters=, [VC Unknown @ 20:10433363-10433423 Q. of type=SYMBOLIC alleles=[G*, <NON_REF>] attr={END=10433423} GT=GT:DP:GQ:MIN_DP:PL 0/0:39:99:36:0,99,1182 filters=], [VC Unknown @ 20:10433382 Q. of type=MIXED alleles=[T*, <NON_REF>, C] attr={AS_RAW_BaseQRankSum=[|-1.9, 1|], AS_RAW_MQ=40862.00|45723.00|0.00, AS_RAW_MQRankSum=[|1.0, 1|], AS_RAW_ReadPosRankSum=[|0.2, 1|], AS_SB_TABLE=[10, 5|11, 4|0, 0], BaseQRankSum=-1.821e+00, DP=66, ExcessHet=3.01, MQRankSum=1.03, RAW_MQ=86585.00, ReadPosRankSum=0.249} GT=GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:SB ./.:15,15,0:.:99:.:0|1:10433382_T_C:632,0,601,680,652,1332:10,5,11,4 ./.:.:39:99:36:.:.:0,99,1182,99,1182,1182 filters=, [VC Unknown @ 20:10433382 Q623.88 of type=SNP alleles=[T*, C] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=-1.900, AS_FS=0.000, AS_MQ=55.21, AS_MQRankSum=1.000, AS_QD=20.80, AS_ReadPosRankSum=0.200, AS_SOR=0.998, BaseQRankSum=-1.821e+00, DP=66, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.250, MQ=53.72, MQRankSum=1.03, QD=20.80, RAW_MQ=86585.00, ReadPosRankSum=0.249, SOR=0.998} GT=GT:AD:DP:GQ:PGT:PID:PL 0/1:15,15:.:99:0|1:10433382_T_C:632,0,601 0/0:36,0:36:99:.:.:0,99,1182 filters=) 0.001s passed
testCombineAnnotationAgainstExpected[7]([[VC Unknown @ 20:10433391 Q602.77 of type=MIXED alleles=[T*, <NON_REF>, C] attr={AS_RAW_BaseQRankSum=[|-0.3, 1|NaN], AS_RAW_MQ=51662.00|52082.00|0.00, AS_RAW_MQRankSum=[|1.3, 1|NaN], AS_RAW_ReadPosRankSum=[|1.5, 1|NaN], AS_SB_TABLE=[14, 4|13, 3|0, 0], BaseQRankSum=-0.284, DP=34, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=1.329, RAW_MQ=103744.00, ReadPosRankSum=1.536} GT=GT:AD:GQ:PGT:PID:PL:SB 0/1:18,16,0:99:0|1:10433382_T_C:631,0,673,685,724,1409:14,4,13,3 filters=, [VC Unknown @ 20:10433363-10433423 Q. of type=SYMBOLIC alleles=[G*, <NON_REF>] attr={END=10433423} GT=[[NA12892 G*/G* GQ 99 DP 39 PL 0,99,1182 {MIN_DP=36}]] filters=], [VC Unknown @ 20:10433391 Q. of type=MIXED alleles=[T*, <NON_REF>, C] attr={AS_RAW_BaseQRankSum=[|-0.3, 1|], AS_RAW_MQ=51662.00|52082.00|0.00, AS_RAW_MQRankSum=[|1.3, 1|], AS_RAW_ReadPosRankSum=[|1.5, 1|], AS_SB_TABLE=[14, 4|13, 3|0, 0], BaseQRankSum=-2.840e-01, DP=70, ExcessHet=3.01, MQRankSum=1.33, RAW_MQ=103744.00, ReadPosRankSum=1.54} GT=GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:SB ./.:18,16,0:.:99:.:0|1:10433382_T_C:631,0,673,685,724,1409:14,4,13,3 ./.:.:39:99:36:.:.:0,99,1182,99,1182,1182 filters=, [VC Unknown @ 20:10433391 Q622.88 of type=SNP alleles=[T*, C] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=-0.300, AS_FS=0.000, AS_MQ=57.05, AS_MQRankSum=1.300, AS_QD=18.32, AS_ReadPosRankSum=1.500, AS_SOR=0.859, BaseQRankSum=-2.840e-01, DP=70, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.250, MQ=55.24, MQRankSum=1.33, QD=18.32, RAW_MQ=103744.00, ReadPosRankSum=1.54, SOR=0.859} GT=GT:AD:DP:GQ:PGT:PID:PL 0/1:18,16:.:99:0|1:10433382_T_C:631,0,673 0/0:36,0:36:99:.:.:0,99,1182 filters=) 0s passed
testCombineAnnotationAgainstExpected[8]([[VC Unknown @ 20:10433468 Q624.77 of type=MIXED alleles=[T*, <NON_REF>, C] attr={AS_RAW_BaseQRankSum=[|-1.4, 1|NaN], AS_RAW_MQ=63049.00|69241.00|0.00, AS_RAW_MQRankSum=[|0.0, 1|NaN], AS_RAW_ReadPosRankSum=[|1.4, 1|NaN], AS_SB_TABLE=[13, 5|12, 8|0, 0], BaseQRankSum=-1.312, DP=38, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=0.076, RAW_MQ=132290.00, ReadPosRankSum=1.463} GT=GT:AD:GQ:PL:SB 0/1:18,20,0:99:653,0,572,707,633,1339:13,5,12,8 filters=, [VC Unknown @ 20:10433461-10433469 Q. of type=SYMBOLIC alleles=[T*, <NON_REF>] attr={END=10433469} GT=GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 filters=], [VC Unknown @ 20:10433468 Q. of type=MIXED alleles=[T*, <NON_REF>, C] attr={AS_RAW_BaseQRankSum=[|-1.4, 1|], AS_RAW_MQ=63049.00|69241.00|0.00, AS_RAW_MQRankSum=[|0.0, 1|], AS_RAW_ReadPosRankSum=[|1.4, 1|], AS_SB_TABLE=[13, 5|12, 8|0, 0], BaseQRankSum=-1.312e+00, DP=68, ExcessHet=3.01, MQRankSum=0.076, RAW_MQ=132290.00, ReadPosRankSum=1.46} GT=GT:AD:DP:GQ:MIN_DP:PL:SB ./.:18,20,0:.:99:.:653,0,572,707,633,1339:13,5,12,8 ./.:.:31:81:30:0,81,1215,81,1215,1215 filters=, [VC Unknown @ 20:10433468 Q644.88 of type=SNP alleles=[T*, C] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=-1.400, AS_FS=2.955, AS_MQ=58.84, AS_MQRankSum=0.000, AS_QD=16.97, AS_ReadPosRankSum=1.400, AS_SOR=0.324, BaseQRankSum=-1.312e+00, DP=68, ExcessHet=3.0103, FS=2.955, MLEAC=1, MLEAF=0.250, MQ=59.00, MQRankSum=0.076, QD=16.97, RAW_MQ=132290.00, ReadPosRankSum=1.46, SOR=0.324} GT=GT:AD:DP:GQ:PL 0/1:18,20:.:99:653,0,572 0/0:30,0:30:81:0,81,1215 filters=) 0.001s passed
testCombineAnnotationAgainstExpected[9]([[VC Unknown @ 20:10433560 Q966.77 of type=MIXED alleles=[C*, <NON_REF>, A] attr={AS_RAW_BaseQRankSum=[|3.4, 1|NaN], AS_RAW_MQ=111600.00|87769.00|0.00, AS_RAW_MQRankSum=[|-1.1, 1|NaN], AS_RAW_ReadPosRankSum=[|1.3, 1|NaN], AS_SB_TABLE=[30, 1|22, 3|0, 0], BaseQRankSum=3.497, DP=56, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=-1.078, RAW_MQ=199369.00, ReadPosRankSum=1.376} GT=GT:AD:GQ:PGT:PID:PL:SB 0/1:31,25,0:99:0|1:10433560_C_A:995,0,3032,1092,3110,4202:30,1,22,3 filters=, [VC Unknown @ 20:10433505-10433707 Q. of type=SYMBOLIC alleles=[T*, <NON_REF>] attr={END=10433707} GT=GT:DP:GQ:MIN_DP:PL 0/0:51:99:39:0,99,1485 filters=], [VC Unknown @ 20:10433560 Q. of type=MIXED alleles=[C*, <NON_REF>, A] attr={AS_RAW_BaseQRankSum=[|3.4, 1|], AS_RAW_MQ=111600.00|87769.00|0.00, AS_RAW_MQRankSum=[|-1.1, 1|], AS_RAW_ReadPosRankSum=[|1.3, 1|], AS_SB_TABLE=[30, 1|22, 3|0, 0], BaseQRankSum=3.50, DP=95, ExcessHet=3.01, MQRankSum=-1.078e+00, RAW_MQ=199369.00, ReadPosRankSum=1.38} GT=GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:SB ./.:31,25,0:.:99:.:0|1:10433560_C_A:995,0,3032,1092,3110,4202:30,1,22,3 ./.:.:51:99:39:.:.:0,99,1485,99,1485,1485 filters=, [VC Unknown @ 20:10433560 Q986.88 of type=SNP alleles=[C*, A] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=3.400, AS_FS=5.027, AS_MQ=59.25, AS_MQRankSum=-1.100, AS_QD=17.63, AS_ReadPosRankSum=1.300, AS_SOR=0.129, BaseQRankSum=3.50, DP=95, ExcessHet=3.0103, FS=5.027, MLEAC=1, MLEAF=0.250, MQ=59.67, MQRankSum=-1.078e+00, QD=17.62, RAW_MQ=199369.00, ReadPosRankSum=1.38, SOR=0.129} GT=GT:AD:DP:GQ:PGT:PID:PL 0/1:31,25:.:99:0|1:10433560_C_A:995,0,3032 0/0:39,0:39:99:.:.:0,99,1485 filters=) 0.001s passed
testFinalizeAnnotationAgainstExpected[0]([[VC Unknown @ 20:10087820-10087822 Q264.73 of type=MIXED alleles=[CAG*, <NON_REF>, C, CAGAG] attr={AS_RAW_BaseQRankSum=[|NaN|-2.1, 1|NaN], AS_RAW_MQ=123769.00|3600.00|46800.00|0.00, AS_RAW_MQRankSum=[|NaN|0.6, 1|NaN], AS_RAW_ReadPosRankSum=[|NaN|-0.4, 1|NaN], AS_SB_TABLE=[17, 18|1, 0|8, 5|0, 0], BaseQRankSum=-2.273, DP=93, ExcessHet=3.0103, MLEAC=[0, 1, 0], MLEAF=[0.00, 0.500, 0.00], MQRankSum=0.678, RAW_MQ=329810.00, ReadPosRankSum=-0.492} GT=GT:AD:GQ:PL:SB 0/2:35,1,13,0:99:302,490,2306,0,1170,1079,483,1995,1169,1922:17,18,9,5 filters=, [VC Unknown @ 20:10087820 Q568.73 of type=MIXED alleles=[C*, <NON_REF>, CAGAG, CAGAGAG] attr={AS_RAW_BaseQRankSum=[|NaN|1.0, 1|NaN], AS_RAW_MQ=97208.00|4441.00|47258.00|0.00, AS_RAW_MQRankSum=[|NaN|-3.1, 1|NaN], AS_RAW_ReadPosRankSum=[|NaN|-0.3, 1|NaN], AS_SB_TABLE=[16, 13|0, 2|12, 12|0, 0], BaseQRankSum=0.955, DP=74, ExcessHet=3.0103, MLEAC=[0, 1, 0], MLEAF=[0.00, 0.500, 0.00], MQRankSum=-3.130, RAW_MQ=211789.00, ReadPosRankSum=-0.254} GT=GT:AD:GQ:PL:SB 0/2:29,2,24,0:99:606,627,1620,0,864,849,697,1597,927,1653:16,13,12,14 filters=], [VC Unknown @ 20:10087820-10087822 Q. of type=MIXED alleles=[CAG*, <NON_REF>, C, CAGAG, CAGAGAG, CAGAGAGAG] attr={AS_RAW_BaseQRankSum=[||1.0, 1||-2.1, 1|], AS_RAW_MQ=220977.00|4441.00|47258.00|3600.00|46800.00|0.00, AS_RAW_MQRankSum=[||-3.1, 1||0.6, 1|], AS_RAW_ReadPosRankSum=[||-0.3, 1||-0.4, 1|], AS_SB_TABLE=[33, 31|0, 2|12, 12|1, 0|8, 5|0, 0], BaseQRankSum=0.955, DP=167, ExcessHet=3.01, MQRankSum=0.678, RAW_MQ=541599.00, ReadPosRankSum=-2.540e-01} GT=GT:AD:GQ:PL:SB ./.:35,0,0,1,13,0:99:302,483,1922,483,1922,1922,490,1995,1995,2306,0,1169,1169,1170,1079,483,1922,1922,1995,1169,1922:17,18,9,5 ./.:29,2,24,0,0,0:99:606,627,1620,0,864,849,697,1597,927,1653,697,1597,927,1653,1653,697,1597,927,1653,1653,1653:16,13,12,14 filters=, [VC Unknown @ 20:10087820 Q892.52 of type=INDEL alleles=[C*, CAG, CAGAGAG] attr={AC=[1, 1], AF=[0.250, 0.250], AN=4, AS_BaseQRankSum=[1.000, -2.100], AS_FS=[0.000, 2.538], AS_MQ=[44.37, 60.00], AS_MQRankSum=[-3.100, 0.600], AS_QD=[6.80, 3.82], AS_ReadPosRankSum=[-0.300, -0.400], AS_SOR=[0.634, 1.096], BaseQRankSum=0.955, DP=167, ExcessHet=4.7712, FS=0.000, MLEAC=[1, 1], MLEAF=[0.250, 0.250], MQ=56.95, MQRankSum=0.678, QD=8.84, RAW_MQ=541599.00, ReadPosRankSum=-2.540e-01, SOR=0.728} GT=GT:AD:GQ:PL 0/2:35,0,13:99:302,483,1922,0,1169,1079 0/1:29,24,0:99:606,0,849,697,927,1653 filters=) 0.002s passed
testFinalizeAnnotationAgainstExpected[10]([[VC Unknown @ 20:10433575 Q1122.77 of type=MIXED alleles=[C*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|3.8, 1|NaN], AS_RAW_MQ=119641.00|100251.00|0.00, AS_RAW_MQRankSum=[|-1.2, 1|NaN], AS_RAW_ReadPosRankSum=[|0.8, 1|NaN], AS_SB_TABLE=[31, 3|26, 4|0, 0], BaseQRankSum=3.811, DP=64, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=-1.123, RAW_MQ=219892.00, ReadPosRankSum=0.830} GT=GT:AD:GQ:PGT:PID:PL:SB 0/1:34,30,0:99:0|1:10433560_C_A:1151,0,3385,1260,3476,4735:31,3,26,4 filters=, [VC Unknown @ 20:10433505-10433707 Q. of type=SYMBOLIC alleles=[T*, <NON_REF>] attr={END=10433707} GT=GT:DP:GQ:MIN_DP:PL 0/0:51:99:39:0,99,1485 filters=], [VC Unknown @ 20:10433575 Q. of type=MIXED alleles=[C*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|3.8, 1|], AS_RAW_MQ=119641.00|100251.00|0.00, AS_RAW_MQRankSum=[|-1.2, 1|], AS_RAW_ReadPosRankSum=[|0.8, 1|], AS_SB_TABLE=[31, 3|26, 4|0, 0], BaseQRankSum=3.81, DP=103, ExcessHet=3.01, MQRankSum=-1.123e+00, RAW_MQ=219892.00, ReadPosRankSum=0.830} GT=GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:SB ./.:34,30,0:.:99:.:0|1:10433560_C_A:1151,0,3385,1260,3476,4735:31,3,26,4 ./.:.:51:99:39:.:.:0,99,1485,99,1485,1485 filters=, [VC Unknown @ 20:10433575 Q1142.88 of type=SNP alleles=[C*, T] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=3.800, AS_FS=1.568, AS_MQ=57.81, AS_MQRankSum=-1.200, AS_QD=17.86, AS_ReadPosRankSum=0.800, AS_SOR=0.375, BaseQRankSum=3.81, DP=103, ExcessHet=3.0103, FS=1.568, MLEAC=1, MLEAF=0.250, MQ=58.62, MQRankSum=-1.123e+00, QD=17.86, RAW_MQ=219892.00, ReadPosRankSum=0.830, SOR=0.375} GT=GT:AD:DP:GQ:PGT:PID:PL 0/1:34,30:.:99:0|1:10433560_C_A:1151,0,3385 0/0:39,0:39:99:.:.:0,99,1485 filters=) 0s passed
testFinalizeAnnotationAgainstExpected[11]([[VC Unknown @ 20:10433594 Q1084.77 of type=MIXED alleles=[C*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|4.8, 1|NaN], AS_RAW_MQ=108841.00|85615.00|0.00, AS_RAW_MQRankSum=[|-2.4, 1|NaN], AS_RAW_ReadPosRankSum=[|-0.6, 1|NaN], AS_SB_TABLE=[28, 3|25, 4|0, 0], BaseQRankSum=4.816, DP=61, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=-2.334, RAW_MQ=195825.00, ReadPosRankSum=-0.502} GT=GT:AD:GQ:PGT:PID:PL:SB 0/1:31,29,0:99:0|1:10433560_C_A:1113,0,3070,1206,3160,4366:28,3,25,4 filters=, [VC Unknown @ 20:10433505-10433707 Q. of type=SYMBOLIC alleles=[T*, <NON_REF>] attr={END=10433707} GT=GT:DP:GQ:MIN_DP:PL 0/0:51:99:39:0,99,1485 filters=], [VC Unknown @ 20:10433594 Q. of type=MIXED alleles=[C*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|4.8, 1|], AS_RAW_MQ=108841.00|85615.00|0.00, AS_RAW_MQRankSum=[|-2.4, 1|], AS_RAW_ReadPosRankSum=[|-0.6, 1|], AS_SB_TABLE=[28, 3|25, 4|0, 0], BaseQRankSum=4.82, DP=100, ExcessHet=3.01, MQRankSum=-2.334e+00, RAW_MQ=195825.00, ReadPosRankSum=-5.020e-01} GT=GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:SB ./.:31,29,0:.:99:.:0|1:10433560_C_A:1113,0,3070,1206,3160,4366:28,3,25,4 ./.:.:51:99:39:.:.:0,99,1485,99,1485,1485 filters=, [VC Unknown @ 20:10433594 Q1104.88 of type=SNP alleles=[C*, T] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=4.800, AS_FS=1.535, AS_MQ=54.33, AS_MQRankSum=-2.400, AS_QD=18.42, AS_ReadPosRankSum=-0.600, AS_SOR=0.415, BaseQRankSum=4.82, DP=100, ExcessHet=3.0103, FS=1.535, MLEAC=1, MLEAF=0.250, MQ=56.66, MQRankSum=-2.334e+00, QD=18.41, RAW_MQ=195825.00, ReadPosRankSum=-5.020e-01, SOR=0.415} GT=GT:AD:DP:GQ:PGT:PID:PL 0/1:31,29:.:99:0|1:10433560_C_A:1113,0,3070 0/0:39,0:39:99:.:.:0,99,1485 filters=) 0.001s passed
testFinalizeAnnotationAgainstExpected[12]([[VC Unknown @ 20:10433955 Q997.73 of type=MIXED alleles=[C*, <NON_REF>, CGTGTGTGTGTAT] attr={AS_RAW_BaseQRankSum=[|0.4, 1|NaN], AS_RAW_MQ=59810.00|39497.00|0.00, AS_RAW_MQRankSum=[|-4.0, 1|NaN], AS_RAW_ReadPosRankSum=[|-0.8, 1|NaN], AS_SB_TABLE=[12, 6|16, 8|0, 0], BaseQRankSum=0.422, DP=47, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=-4.001, RAW_MQ=117307.00, ReadPosRankSum=-0.789} GT=GT:AD:GQ:PL:SB 0/1:18,24,0:99:1035,0,1217,1090,1298,2389:12,6,16,8 filters=, [VC Unknown @ 20:10433722-10433955 Q. of type=SYMBOLIC alleles=[A*, <NON_REF>] attr={END=10433955} GT=GT:DP:GQ:MIN_DP:PL 0/0:59:99:37:0,99,1485 filters=], [VC Unknown @ 20:10433955 Q. of type=MIXED alleles=[C*, <NON_REF>, CGTGTGTGTGTAT] attr={AS_RAW_BaseQRankSum=[|0.4, 1|], AS_RAW_MQ=59810.00|39497.00|0.00, AS_RAW_MQRankSum=[|-4.0, 1|], AS_RAW_ReadPosRankSum=[|-0.8, 1|], AS_SB_TABLE=[12, 6|16, 8|0, 0], BaseQRankSum=0.422, DP=84, ExcessHet=3.01, MQRankSum=-4.001e+00, RAW_MQ=117307.00, ReadPosRankSum=-7.890e-01} GT=GT:AD:DP:GQ:MIN_DP:PL:SB ./.:18,24,0:.:99:.:1035,0,1217,1090,1298,2389:12,6,16,8 ./.:.:59:99:37:0,99,1485,99,1485,1485 filters=, [VC Unknown @ 20:10433955 Q1026.91 of type=INDEL alleles=[C*, CGTGTGTGTGTAT] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=0.400, AS_FS=0.000, AS_MQ=40.57, AS_MQRankSum=-4.000, AS_QD=24.45, AS_ReadPosRankSum=-0.800, AS_SOR=0.710, BaseQRankSum=0.422, DP=84, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.250, MQ=49.96, MQRankSum=-4.001e+00, QD=24.45, RAW_MQ=117307.00, ReadPosRankSum=-7.890e-01, SOR=0.710} GT=GT:AD:DP:GQ:PL 0/1:18,24:.:99:1035,0,1217 0/0:37,0:37:99:0,99,1485 filters=) 0s passed
testFinalizeAnnotationAgainstExpected[13]([[VC Unknown @ 20:10434177 Q1446.77 of type=MIXED alleles=[A*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|0.9, 1|NaN], AS_RAW_MQ=108000.00|133784.00|0.00, AS_RAW_MQRankSum=[|-2.5, 1|NaN], AS_RAW_ReadPosRankSum=[|-0.9, 1|NaN], AS_SB_TABLE=[15, 15|23, 20|0, 0], BaseQRankSum=0.903, DP=74, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=-2.473, RAW_MQ=245384.00, ReadPosRankSum=-0.891} GT=GT:AD:GQ:PL:SB 0/1:30,43,0:99:1475,0,936,1565,1066,2631:15,15,23,20 filters=, [VC Unknown @ 20:10434083-10436207 Q. of type=SYMBOLIC alleles=[G*, <NON_REF>] attr={END=10436207} GT=GT:DP:GQ:MIN_DP:PL 0/0:75:99:37:0,102,1530 filters=], [VC Unknown @ 20:10434177 Q. of type=MIXED alleles=[A*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|0.9, 1|], AS_RAW_MQ=108000.00|133784.00|0.00, AS_RAW_MQRankSum=[|-2.5, 1|], AS_RAW_ReadPosRankSum=[|-0.9, 1|], AS_SB_TABLE=[15, 15|23, 20|0, 0], BaseQRankSum=0.903, DP=111, ExcessHet=3.01, MQRankSum=-2.473e+00, RAW_MQ=245384.00, ReadPosRankSum=-8.910e-01} GT=GT:AD:DP:GQ:MIN_DP:PL:SB ./.:30,43,0:.:99:.:1475,0,936,1565,1066,2631:15,15,23,20 ./.:.:75:99:37:0,102,1530,102,1530,1530 filters=, [VC Unknown @ 20:10434177 Q1466.88 of type=SNP alleles=[A*, T] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=0.900, AS_FS=0.888, AS_MQ=55.78, AS_MQRankSum=-2.500, AS_QD=20.10, AS_ReadPosRankSum=-0.900, AS_SOR=0.836, BaseQRankSum=0.903, DP=111, ExcessHet=3.0103, FS=0.888, MLEAC=1, MLEAF=0.250, MQ=57.58, MQRankSum=-2.473e+00, QD=20.09, RAW_MQ=245384.00, ReadPosRankSum=-8.910e-01, SOR=0.836} GT=GT:AD:DP:GQ:PL 0/1:30,43:.:99:1475,0,936 0/0:37,0:37:99:0,102,1530 filters=) 0.001s passed
testFinalizeAnnotationAgainstExpected[14]([[VC Unknown @ 20:10434384-10434385 Q752.73 of type=MIXED alleles=[TA*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|-0.1, 1|NaN], AS_RAW_MQ=123769.00|118800.00|0.00, AS_RAW_MQRankSum=[|1.0, 1|NaN], AS_RAW_ReadPosRankSum=[|0.4, 1|NaN], AS_SB_TABLE=[22, 13|21, 12|0, 0], BaseQRankSum=-0.100, DP=71, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=1.000, RAW_MQ=253369.00, ReadPosRankSum=0.497} GT=GT:AD:GQ:PL:SB 0/1:35,33,0:99:790,0,846,895,945,1840:22,13,21,12 filters=, [VC Unknown @ 20:10434083-10436207 Q. of type=SYMBOLIC alleles=[G*, <NON_REF>] attr={END=10436207} GT=GT:DP:GQ:MIN_DP:PL 0/0:75:99:37:0,102,1530 filters=], [VC Unknown @ 20:10434384-10434385 Q. of type=MIXED alleles=[TA*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|-0.1, 1|], AS_RAW_MQ=123769.00|118800.00|0.00, AS_RAW_MQRankSum=[|1.0, 1|], AS_RAW_ReadPosRankSum=[|0.4, 1|], AS_SB_TABLE=[22, 13|21, 12|0, 0], BaseQRankSum=-1.000e-01, DP=108, ExcessHet=3.01, MQRankSum=1.00, RAW_MQ=253369.00, ReadPosRankSum=0.497} GT=GT:AD:DP:GQ:MIN_DP:PL:SB ./.:35,33,0:.:99:.:790,0,846,895,945,1840:22,13,21,12 ./.:.:75:99:37:0,102,1530,102,1530,1530 filters=, [VC Unknown @ 20:10434384-10434385 Q781.88 of type=INDEL alleles=[TA*, T] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=-0.100, AS_FS=0.000, AS_MQ=60.00, AS_MQRankSum=1.000, AS_QD=11.50, AS_ReadPosRankSum=0.400, AS_SOR=0.723, BaseQRankSum=-1.000e-01, DP=108, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.250, MQ=59.74, MQRankSum=1.00, QD=11.50, RAW_MQ=253369.00, ReadPosRankSum=0.497, SOR=0.723} GT=GT:AD:DP:GQ:PL 0/1:35,33:.:99:790,0,846 0/0:37,0:37:99:0,102,1530 filters=) 0.001s passed
testFinalizeAnnotationAgainstExpected[15]([[VC Unknown @ 20:10435067-10435069 Q1416.73 of type=MIXED alleles=[GTA*, <NON_REF>, G] attr={AS_RAW_BaseQRankSum=[|2.6, 1|NaN], AS_RAW_MQ=108000.00|133200.00|0.00, AS_RAW_MQRankSum=[|0.0, 1|NaN], AS_RAW_ReadPosRankSum=[|-0.2, 1|NaN], AS_SB_TABLE=[15, 15|22, 15|0, 0], BaseQRankSum=2.601, DP=67, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=0.000, RAW_MQ=241200.00, ReadPosRankSum=-0.183} GT=GT:AD:GQ:PL:SB 0/1:30,37,0:99:1454,0,1191,1544,1303,2847:15,15,22,15 filters=, [VC Unknown @ 20:10434083-10436207 Q. of type=SYMBOLIC alleles=[G*, <NON_REF>] attr={END=10436207} GT=GT:DP:GQ:MIN_DP:PL 0/0:75:99:37:0,102,1530 filters=], [VC Unknown @ 20:10435067-10435069 Q. of type=MIXED alleles=[GTA*, <NON_REF>, G] attr={AS_RAW_BaseQRankSum=[|2.6, 1|], AS_RAW_MQ=108000.00|133200.00|0.00, AS_RAW_MQRankSum=[|0.0, 1|], AS_RAW_ReadPosRankSum=[|-0.2, 1|], AS_SB_TABLE=[15, 15|22, 15|0, 0], BaseQRankSum=2.60, DP=104, ExcessHet=3.01, MQRankSum=0.00, RAW_MQ=241200.00, ReadPosRankSum=-1.830e-01} GT=GT:AD:DP:GQ:MIN_DP:PL:SB ./.:30,37,0:.:99:.:1454,0,1191,1544,1303,2847:15,15,22,15 ./.:.:75:99:37:0,102,1530,102,1530,1530 filters=, [VC Unknown @ 20:10435067-10435069 Q1445.88 of type=INDEL alleles=[GTA*, G] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=2.600, AS_FS=3.289, AS_MQ=60.00, AS_MQRankSum=0.000, AS_QD=21.58, AS_ReadPosRankSum=-0.200, AS_SOR=1.121, BaseQRankSum=2.60, DP=104, ExcessHet=3.0103, FS=3.289, MLEAC=1, MLEAF=0.250, MQ=60.00, MQRankSum=0.00, QD=21.58, RAW_MQ=241200.00, ReadPosRankSum=-1.830e-01, SOR=1.121} GT=GT:AD:DP:GQ:PL 0/1:30,37:.:99:1454,0,1191 0/0:37,0:37:99:0,102,1530 filters=) 0s passed
testFinalizeAnnotationAgainstExpected[16]([[VC Unknown @ 20:10434258 Q1214.77 of type=MIXED alleles=[G*, <NON_REF>, A] attr={AS_RAW_BaseQRankSum=[|3.0, 1|NaN], AS_RAW_MQ=109369.00|106451.00|0.00, AS_RAW_MQRankSum=[|-2.9, 1|NaN], AS_RAW_ReadPosRankSum=[|-0.2, 1|NaN], AS_SB_TABLE=[19, 12|24, 14|0, 0], BaseQRankSum=3.063, DP=70, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=-2.871, RAW_MQ=219420.00, ReadPosRankSum=-0.155} GT=GT:AD:GQ:PL:SB 0/1:31,38,0:99:1243,0,1003,1337,1118,2455:19,12,24,14 filters=, [VC Unknown @ 20:10434083-10436207 Q. of type=SYMBOLIC alleles=[G*, <NON_REF>] attr={END=10436207} GT=GT:DP:GQ:MIN_DP:PL 0/0:75:99:37:0,102,1530 filters=], [VC Unknown @ 20:10434258 Q. of type=MIXED alleles=[G*, <NON_REF>, A] attr={AS_RAW_BaseQRankSum=[|3.0, 1|], AS_RAW_MQ=109369.00|106451.00|0.00, AS_RAW_MQRankSum=[|-2.9, 1|], AS_RAW_ReadPosRankSum=[|-0.2, 1|], AS_SB_TABLE=[19, 12|24, 14|0, 0], BaseQRankSum=3.06, DP=107, ExcessHet=3.01, MQRankSum=-2.871e+00, RAW_MQ=219420.00, ReadPosRankSum=-1.550e-01} GT=GT:AD:DP:GQ:MIN_DP:PL:SB ./.:31,38,0:.:99:.:1243,0,1003,1337,1118,2455:19,12,24,14 ./.:.:75:99:37:0,102,1530,102,1530,1530 filters=, [VC Unknown @ 20:10434258 Q1234.88 of type=SNP alleles=[G*, A] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=3.000, AS_FS=0.000, AS_MQ=52.93, AS_MQRankSum=-2.900, AS_QD=17.90, AS_ReadPosRankSum=-0.200, AS_SOR=0.776, BaseQRankSum=3.06, DP=107, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.250, MQ=55.99, MQRankSum=-2.871e+00, QD=17.90, RAW_MQ=219420.00, ReadPosRankSum=-1.550e-01, SOR=0.776} GT=GT:AD:DP:GQ:PL 0/1:31,38:.:99:1243,0,1003 0/0:37,0:37:99:0,102,1530 filters=) 0.001s passed
testFinalizeAnnotationAgainstExpected[17]([[VC Unknown @ 20:10436227-10436247 Q1187.73 of type=MIXED alleles=[TTTTATTTATTTATTTATTTA*, <NON_REF>, T, TTTTATTTATTTATTTATTTATTTA] attr={AS_RAW_BaseQRankSum=|||, AS_RAW_MQ=3600.00|25702.00|19682.00|0.00, AS_RAW_MQRankSum=|||, AS_RAW_ReadPosRankSum=|||, AS_SB_TABLE=[1, 0|14, 10|4, 3|0, 0], BaseQRankSum=-1.450, DP=75, ExcessHet=3.0103, MLEAC=[1, 1, 0], MLEAF=[0.500, 0.500, 0.00], MQRankSum=-1.660, RAW_MQ=201025.00, ReadPosRankSum=1.303} GT=GT:AD:GQ:PL:SB 1/2:1,24,7,0:99:1225,241,589,947,0,970,1258,491,1017,1480:1,0,18,13 filters=, [VC Unknown @ 20:10436227 Q387.74 of type=MIXED alleles=[T*, <NON_REF>, TTTTA] attr={AS_RAW_BaseQRankSum=||, AS_RAW_MQ=0.00|29194.00|0.00, AS_RAW_MQRankSum=||, AS_RAW_ReadPosRankSum=||, AS_SB_TABLE=[0, 0|7, 3|0, 0], DP=33, ExcessHet=3.0103, MLEAC=[2, 0], MLEAF=[1.00, 0.00], RAW_MQ=111994.00} GT=GT:AD:GQ:PL:SB 1/1:0,10,0:29:425,29,0,427,30,428:0,0,7,3 filters=], [VC Unknown @ 20:10436227-10436247 Q. of type=MIXED alleles=[TTTTATTTATTTATTTATTTA*, <NON_REF>, T, TTTTATTTATTTATTTATTTATTTA] attr={AS_RAW_BaseQRankSum=|||, AS_RAW_MQ=3600.00|48876.00|25702.00|0.00, AS_RAW_MQRankSum=|||, AS_RAW_ReadPosRankSum=|||, AS_SB_TABLE=[1, 0|11, 6|14, 10|0, 0], BaseQRankSum=-1.450e+00, DP=108, ExcessHet=3.01, MQRankSum=-1.660e+00, RAW_MQ=313019.00, ReadPosRankSum=1.30} GT=GT:AD:GQ:PL:SB ./.:1,7,24,0:99:1225,947,970,241,0,589,1258,1017,491,1480:1,0,18,13 ./.:0,10,0,0:29:425,29,0,427,30,428,427,30,428,428:0,0,7,3 filters=, [VC Unknown @ 20:10436227-10436247 Q1627.36 of type=INDEL alleles=[TTTTATTTATTTATTTATTTA*, T, TTTTATTTATTTATTTATTTATTTA] attr={AC=[3, 1], AF=[0.750, 0.250], AN=4, AS_BaseQRankSum=[., .], AS_FS=[0.000, 0.000], AS_MQ=[53.62, 32.72], AS_MQRankSum=[., .], AS_QD=[27.24, 28.20], AS_ReadPosRankSum=[., .], AS_SOR=[0.551, 0.382], BaseQRankSum=-1.450e+00, DP=108, ExcessHet=3.0103, FS=0.000, MLEAC=[3, 1], MLEAF=[0.750, 0.250], MQ=53.84, MQRankSum=-1.660e+00, QD=25.00, RAW_MQ=313019.00, ReadPosRankSum=1.30, SOR=0.460} GT=GT:AD:GQ:PL 1/2:1,7,24:99:1225,947,970,241,0,589 1/1:0,10,0:29:425,29,0,427,30,428 filters=) 0s passed
testFinalizeAnnotationAgainstExpected[18]([[VC Unknown @ 20:10684106-10684118 Q0.00 of type=MIXED alleles=[CCTTTCTTTCTTT*, <NON_REF>, C, CCTTTCTTT] attr={AS_RAW_BaseQRankSum=|NaN|NaN|NaN, AS_RAW_MQ=101641.00|0.00|0.00|0.00, AS_RAW_MQRankSum=|NaN|NaN|NaN, AS_RAW_ReadPosRankSum=|NaN|NaN|NaN, AS_SB_TABLE=[9, 20|0, 0|0, 0|0, 0], DP=60, ExcessHet=3.0103, MLEAC=[0, 0, 0], MLEAF=[0.00, 0.00, 0.00], RAW_MQ=196687.00} GT=GT:AD:GQ:PL:SB 0/0:29,0,0,0:84:0,101,3282,84,1698,1592,112,2553,1707,2450:9,20,0,0 filters=, [VC Unknown @ 20:10684106 Q. of type=SYMBOLIC alleles=[C*, <NON_REF>] attr={END=10684106} GT=GT:DP:GQ:MIN_DP:PL 0/0:46:99:46:0,108,1620 filters=], [VC Unknown @ 20:10684106-10684118 Q. of type=MIXED alleles=[CCTTTCTTTCTTT*, <NON_REF>, C, CCTTTCTTT] attr={AS_RAW_BaseQRankSum=|||, AS_RAW_MQ=101641.00|0.00|0.00|0.00, AS_RAW_MQRankSum=|||, AS_RAW_ReadPosRankSum=|||, AS_SB_TABLE=[9, 20|0, 0|0, 0|0, 0], DP=106, ExcessHet=3.01, RAW_MQ=196687.00} GT=GT:AD:DP:GQ:MIN_DP:PL:SB ./.:29,0,0,0:.:84:.:0,101,3282,84,1698,1592,112,2553,1707,2450:9,20,0,0 ./.:.:46:99:46:0,108,1620,108,1620,1620,108,1620,1620,1620 filters=, null) 0.001s passed
testFinalizeAnnotationAgainstExpected[1]([[VC Unknown @ 20:10433312-10433319 Q0.00 of type=MIXED alleles=[CAAAAAAA*, <NON_REF>, C, CAAAAAA] attr={AS_RAW_BaseQRankSum=|NaN|NaN|NaN, AS_RAW_MQ=29659.00|0.00|0.00|0.00, AS_RAW_MQRankSum=|NaN|NaN|NaN, AS_RAW_ReadPosRankSum=|NaN|NaN|NaN, AS_SB_TABLE=[6, 10|0, 0|0, 0|0, 0], DP=37, ExcessHet=3.0103, MLEAC=[0, 0, 0], MLEAF=[0.00, 0.00, 0.00], RAW_MQ=83187.00} GT=GT:AD:GQ:PL:SB 0/0:16,0,0,0:48:0,74,1123,48,615,553,75,891,606,839:6,10,0,0 filters=, [VC Unknown @ 20:10433312-10433319 Q0.00 of type=MIXED alleles=[CAAAAAAA*, <NON_REF>, C, CAAAAAA] attr={AS_RAW_BaseQRankSum=|NaN|NaN|NaN, AS_RAW_MQ=46939.00|0.00|1682.00|0.00, AS_RAW_MQRankSum=|NaN|NaN|NaN, AS_RAW_ReadPosRankSum=|NaN|NaN|NaN, AS_SB_TABLE=[13, 10|0, 0|1, 1|0, 0], BaseQRankSum=1.588, DP=43, ExcessHet=3.0103, MLEAC=[0, 0, 0], MLEAF=[0.00, 0.00, 0.00], MQRankSum=-1.259, RAW_MQ=95936.00, ReadPosRankSum=0.333} GT=GT:AD:GQ:PL:SB 0/0:23,0,2,0:10:0,81,1139,10,811,747,81,1026,798,979:13,10,1,1 filters=], [VC Unknown @ 20:10433312-10433319 Q. of type=MIXED alleles=[CAAAAAAA*, <NON_REF>, C, CAAAAAA] attr={AS_RAW_BaseQRankSum=|||, AS_RAW_MQ=76598.00|0.00|1682.00|0.00, AS_RAW_MQRankSum=|||, AS_RAW_ReadPosRankSum=|||, AS_SB_TABLE=[19, 20|0, 0|1, 1|0, 0], BaseQRankSum=1.59, DP=80, ExcessHet=3.01, MQRankSum=-1.259e+00, RAW_MQ=179123.00, ReadPosRankSum=0.333} GT=GT:AD:GQ:PL:SB ./.:16,0,0,0:48:0,74,1123,48,615,553,75,891,606,839:6,10,0,0 ./.:23,0,2,0:10:0,81,1139,10,811,747,81,1026,798,979:13,10,1,1 filters=, null) 0s passed
testFinalizeAnnotationAgainstExpected[2]([[VC Unknown @ 20:10433322 Q86.73 of type=MIXED alleles=[A*, <NON_REF>, AT] attr={AS_RAW_BaseQRankSum=[|2.5, 1|NaN], AS_RAW_MQ=14418.00|9723.00|0.00, AS_RAW_MQRankSum=[|1.1, 1|NaN], AS_RAW_ReadPosRankSum=[|2.0, 1|NaN], AS_SB_TABLE=[5, 6|2, 3|0, 0], BaseQRankSum=2.564, DP=35, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=1.122, RAW_MQ=67710.00, ReadPosRankSum=2.044} GT=GT:AD:GQ:PL:SB 0/1:11,5,0:99:124,0,369,158,384,542:5,6,2,3 filters=, [VC Unknown @ 20:10433322 Q412.79 of type=MIXED alleles=[A*, <NON_REF>, AT, ATAT] attr={AS_RAW_BaseQRankSum=[|0.8, 1|NaN|NaN], AS_RAW_MQ=3364.00|31589.00|2523.00|0.00, AS_RAW_MQRankSum=[|2.2, 1|NaN|NaN], AS_RAW_ReadPosRankSum=[|1.9, 1|NaN|NaN], AS_SB_TABLE=[2, 2|6, 6|2, 1|0, 0], BaseQRankSum=0.877, DP=42, ExcessHet=3.0103, MLEAC=[1, 0, 0], MLEAF=[0.500, 0.00, 0.00], MQRankSum=1.895, RAW_MQ=86818.00, ReadPosRankSum=1.704} GT=GT:AD:GQ:PL:SB 0/1:4,12,3,0:19:450,0,46,298,19,576,442,117,506,617:2,2,8,7 filters=], [VC Unknown @ 20:10433322 Q. of type=MIXED alleles=[A*, <NON_REF>, AT, ATAT] attr={AS_RAW_BaseQRankSum=[|0.8, 1, 2.5, 1||], AS_RAW_MQ=17782.00|41312.00|2523.00|0.00, AS_RAW_MQRankSum=[|1.1, 1, 2.2, 1||], AS_RAW_ReadPosRankSum=[|1.9, 1, 2.0, 1||], AS_SB_TABLE=[7, 8|8, 9|2, 1|0, 0], BaseQRankSum=2.56, DP=77, ExcessHet=3.01, MQRankSum=1.90, RAW_MQ=154528.00, ReadPosRankSum=2.04} GT=GT:AD:GQ:PL:SB ./.:11,5,0,0:99:124,0,369,158,384,542,158,384,542,542:5,6,2,3 ./.:4,12,3,0:19:450,0,46,298,19,576,442,117,506,617:2,2,8,7 filters=, [VC Unknown @ 20:10433322 Q564.50 of type=INDEL alleles=[A*, AT] attr={AC=2, AF=0.500, AN=4, AS_BaseQRankSum=1.650, AS_FS=0.000, AS_MQ=49.30, AS_MQRankSum=1.650, AS_QD=13.75, AS_ReadPosRankSum=1.950, AS_SOR=0.681, BaseQRankSum=2.56, DP=77, ExcessHet=4.7712, FS=0.000, MLEAC=2, MLEAF=0.500, MQ=44.80, MQRankSum=1.90, QD=17.64, RAW_MQ=154528.00, ReadPosRankSum=2.04, SOR=0.582} GT=GT:AD:GQ:PL 0/1:11,5:99:124,0,369 0/1:4,12:46:450,0,46 filters=) 0.001s passed
testFinalizeAnnotationAgainstExpected[3]([[VC Unknown @ 20:10433324 Q199.77 of type=MIXED alleles=[A*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|2.2, 1|NaN], AS_RAW_MQ=11895.00|10564.00|0.00, AS_RAW_MQRankSum=[|0.5, 1|NaN], AS_RAW_ReadPosRankSum=[|1.5, 1|NaN], AS_SB_TABLE=[2, 6|2, 4|0, 0], BaseQRankSum=2.279, DP=33, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=0.584, RAW_MQ=60510.00, ReadPosRankSum=1.543} GT=GT:AD:GQ:PGT:PID:PL:SB 0/1:8,6,0:99:0|1:10433324_A_T:228,0,275,252,294,546:2,6,2,4 filters=, [VC Unknown @ 20:10433324 Q848.77 of type=MIXED alleles=[A*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=||, AS_RAW_MQ=841.00|38317.00|0.00, AS_RAW_MQRankSum=||, AS_RAW_ReadPosRankSum=||, AS_SB_TABLE=[0, 1|11, 9|0, 0], BaseQRankSum=1.458, DP=40, ExcessHet=3.0103, MLEAC=[2, 0], MLEAF=[1.00, 0.00], MQRankSum=0.871, RAW_MQ=79618.00, ReadPosRankSum=1.736} GT=GT:AD:GQ:PGT:PID:PL:SB 1/1:1,20,0:53:0|1:10433324_A_T:877,53,0,880,61,888:0,1,11,9 filters=], [VC Unknown @ 20:10433324 Q. of type=MIXED alleles=[A*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|2.2, 1|], AS_RAW_MQ=12736.00|48881.00|0.00, AS_RAW_MQRankSum=[|0.5, 1|], AS_RAW_ReadPosRankSum=[|1.5, 1|], AS_SB_TABLE=[2, 7|13, 13|0, 0], BaseQRankSum=2.28, DP=73, ExcessHet=3.01, MQRankSum=0.871, RAW_MQ=140128.00, ReadPosRankSum=1.74} GT=GT:AD:GQ:PGT:PID:PL:SB ./.:8,6,0:99:0|1:10433324_A_T:228,0,275,252,294,546:2,6,2,4 ./.:1,20,0:53:0|1:10433324_A_T:877,53,0,880,61,888:0,1,11,9 filters=, [VC Unknown @ 20:10433324 Q1091.09 of type=SNP alleles=[A*, T] attr={AC=3, AF=0.750, AN=4, AS_BaseQRankSum=2.200, AS_FS=6.118, AS_MQ=43.36, AS_MQRankSum=0.500, AS_QD=31.17, AS_ReadPosRankSum=1.500, AS_SOR=0.132, BaseQRankSum=2.28, DP=73, ExcessHet=3.0103, FS=6.118, MLEAC=3, MLEAF=0.750, MQ=43.81, MQRankSum=0.871, QD=31.17, RAW_MQ=140128.00, ReadPosRankSum=1.74, SOR=0.132} GT=GT:AD:GQ:PGT:PID:PL 0/1:8,6:99:0|1:10433324_A_T:228,0,275 1/1:1,20:53:1|1:10433324_A_T:877,53,0 filters=) 0s passed
testFinalizeAnnotationAgainstExpected[4]([[VC Unknown @ 20:10433326 Q199.77 of type=MIXED alleles=[A*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|0.8, 1|NaN], AS_RAW_MQ=11895.00|10564.00|0.00, AS_RAW_MQRankSum=[|0.5, 1|NaN], AS_RAW_ReadPosRankSum=[|1.4, 1|NaN], AS_SB_TABLE=[2, 6|2, 4|0, 0], BaseQRankSum=0.874, DP=31, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=0.584, RAW_MQ=53310.00, ReadPosRankSum=1.403} GT=GT:AD:GQ:PGT:PID:PL:SB 0/1:8,6,0:99:0|1:10433324_A_T:228,0,275,252,293,546:2,6,2,4 filters=, [VC Unknown @ 20:10433326 Q848.77 of type=MIXED alleles=[A*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=||, AS_RAW_MQ=841.00|38317.00|0.00, AS_RAW_MQRankSum=||, AS_RAW_ReadPosRankSum=||, AS_SB_TABLE=[0, 1|11, 9|0, 0], BaseQRankSum=1.537, DP=36, ExcessHet=3.0103, MLEAC=[2, 0], MLEAF=[1.00, 0.00], MQRankSum=0.871, RAW_MQ=65218.00, ReadPosRankSum=1.736} GT=GT:AD:GQ:PGT:PID:PL:SB 1/1:1,20,0:53:0|1:10433324_A_T:877,53,0,881,61,888:0,1,11,9 filters=], [VC Unknown @ 20:10433326 Q. of type=MIXED alleles=[A*, <NON_REF>, T] attr={AS_RAW_BaseQRankSum=[|0.8, 1|], AS_RAW_MQ=12736.00|48881.00|0.00, AS_RAW_MQRankSum=[|0.5, 1|], AS_RAW_ReadPosRankSum=[|1.4, 1|], AS_SB_TABLE=[2, 7|13, 13|0, 0], BaseQRankSum=1.54, DP=67, ExcessHet=3.01, MQRankSum=0.871, RAW_MQ=118528.00, ReadPosRankSum=1.74} GT=GT:AD:GQ:PGT:PID:PL:SB ./.:8,6,0:99:0|1:10433324_A_T:228,0,275,252,293,546:2,6,2,4 ./.:1,20,0:53:0|1:10433324_A_T:877,53,0,881,61,888:0,1,11,9 filters=, [VC Unknown @ 20:10433326 Q1091.09 of type=SNP alleles=[A*, T] attr={AC=3, AF=0.750, AN=4, AS_BaseQRankSum=0.800, AS_FS=6.118, AS_MQ=43.36, AS_MQRankSum=0.500, AS_QD=31.17, AS_ReadPosRankSum=1.400, AS_SOR=0.132, BaseQRankSum=1.54, DP=67, ExcessHet=3.0103, FS=6.118, MLEAC=3, MLEAF=0.750, MQ=42.06, MQRankSum=0.871, QD=31.17, RAW_MQ=118528.00, ReadPosRankSum=1.74, SOR=0.132} GT=GT:AD:GQ:PGT:PID:PL 0/1:8,6:99:0|1:10433324_A_T:228,0,275 1/1:1,20:53:1|1:10433324_A_T:877,53,0 filters=) 0.001s passed
testFinalizeAnnotationAgainstExpected[5]([[VC Unknown @ 20:10433328 Q881.73 of type=MIXED alleles=[A*, <NON_REF>, AATATAT, AATATATAT, ATATAT, ATATATAT, T] attr={AS_RAW_BaseQRankSum=||||||, AS_RAW_MQ=0.00|10564.00|2523.00|0.00|0.00|0.00|0.00, AS_RAW_MQRankSum=||||||, AS_RAW_ReadPosRankSum=||||||, AS_SB_TABLE=[0, 0|2, 4|1, 2|0, 0|0, 0|0, 0|0, 0], DP=30, ExcessHet=3.0103, MLEAC=[1, 1, 0, 0, 0, 0], MLEAF=[0.500, 0.500, 0.00, 0.00, 0.00, 0.00], RAW_MQ=49710.00} GT=GT:AD:GQ:PL:SB 1/2:0,6,3,0,0,0,0:91:919,177,246,420,0,500,470,91,514,592,483,122,379,428,563,513,192,384,470,576,640,676,211,530,616,595,658,804:0,0,3,6 filters=, [VC Unknown @ 20:10433328 Q1153.73 of type=MIXED alleles=[A*, <NON_REF>, AATATAT, AATATATAT, AATATATATAT, T] attr={AS_RAW_BaseQRankSum=|||||, AS_RAW_MQ=0.00|38317.00|0.00|0.00|0.00|0.00, AS_RAW_MQRankSum=|||||, AS_RAW_ReadPosRankSum=|||||, AS_SB_TABLE=[0, 0|11, 9|0, 0|0, 0|0, 0|0, 0], DP=36, ExcessHet=3.0103, MLEAC=[2, 0, 0, 0, 0], MLEAF=[1.00, 0.00, 0.00, 0.00, 0.00], RAW_MQ=65218.00} GT=GT:AD:GQ:PL:SB 1/1:0,20,0,0,0,0:74:1191,74,0,1085,90,1328,951,76,1182,1193,1147,93,1334,1214,1394,1132,93,1334,1213,1381,1376:0,0,11,9 filters=], [VC Unknown @ 20:10433328 Q. of type=MIXED alleles=[A*, <NON_REF>, AATATAT, AATATATAT, AATATATATAT, ATATAT, ATATATAT, T] attr={AS_RAW_BaseQRankSum=|||||||, AS_RAW_MQ=0.00|48881.00|0.00|0.00|0.00|2523.00|0.00|0.00, AS_RAW_MQRankSum=|||||||, AS_RAW_ReadPosRankSum=|||||||, AS_SB_TABLE=[0, 0|13, 13|0, 0|0, 0|0, 0|1, 2|0, 0|0, 0], DP=66, ExcessHet=3.01, RAW_MQ=114928.00} GT=GT:AD:GQ:PL:SB ./.:0,6,0,0,0,3,0,0:91:919,177,246,470,91,592,513,192,470,640,676,211,616,658,804,420,0,514,384,530,500,483,122,428,576,595,379,563,676,211,616,658,804,530,595,804:0,0,3,6 ./.:0,20,0,0,0,0,0,0:74:1191,74,0,1085,90,1328,951,76,1182,1193,1147,93,1334,1214,1394,1132,93,1334,1213,1381,1376,1132,93,1334,1213,1381,1376,1376,1132,93,1334,1213,1381,1376,1376,1376:0,0,11,9 filters=, [VC Unknown @ 20:10433328 Q2087.37 of type=MIXED alleles=[A*, ATATAT, T] attr={AC=[3, 1], AF=[0.750, 0.250], AN=4, AS_BaseQRankSum=[., .], AS_FS=[0.000, 0.000], AS_MQ=[43.36, 29.00], AS_MQRankSum=[., .], AS_QD=[25.36, 28.73], AS_ReadPosRankSum=[., .], AS_SOR=[0.693, 1.179], DP=66, ExcessHet=3.0103, FS=0.000, MLEAC=[3, 1], MLEAF=[0.750, 0.250], MQ=41.73, QD=30.97, RAW_MQ=114928.00, SOR=0.760} GT=GT:AD:GQ:PL 1/2:0,6,3:99:919,177,246,420,0,500 1/1:0,20,0:74:1191,74,0,1132,93,1376 filters=) 0.002s passed
testFinalizeAnnotationAgainstExpected[6]([[VC Unknown @ 20:10433382 Q603.77 of type=MIXED alleles=[T*, <NON_REF>, C] attr={AS_RAW_BaseQRankSum=[|-1.9, 1|NaN], AS_RAW_MQ=40862.00|45723.00|0.00, AS_RAW_MQRankSum=[|1.0, 1|NaN], AS_RAW_ReadPosRankSum=[|0.2, 1|NaN], AS_SB_TABLE=[10, 5|11, 4|0, 0], BaseQRankSum=-1.821, DP=30, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=1.033, RAW_MQ=86585.00, ReadPosRankSum=0.249} GT=GT:AD:GQ:PGT:PID:PL:SB 0/1:15,15,0:99:0|1:10433382_T_C:632,0,601,680,652,1332:10,5,11,4 filters=, [VC Unknown @ 20:10433363-10433423 Q. of type=SYMBOLIC alleles=[G*, <NON_REF>] attr={END=10433423} GT=GT:DP:GQ:MIN_DP:PL 0/0:39:99:36:0,99,1182 filters=], [VC Unknown @ 20:10433382 Q. of type=MIXED alleles=[T*, <NON_REF>, C] attr={AS_RAW_BaseQRankSum=[|-1.9, 1|], AS_RAW_MQ=40862.00|45723.00|0.00, AS_RAW_MQRankSum=[|1.0, 1|], AS_RAW_ReadPosRankSum=[|0.2, 1|], AS_SB_TABLE=[10, 5|11, 4|0, 0], BaseQRankSum=-1.821e+00, DP=66, ExcessHet=3.01, MQRankSum=1.03, RAW_MQ=86585.00, ReadPosRankSum=0.249} GT=GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:SB ./.:15,15,0:.:99:.:0|1:10433382_T_C:632,0,601,680,652,1332:10,5,11,4 ./.:.:39:99:36:.:.:0,99,1182,99,1182,1182 filters=, [VC Unknown @ 20:10433382 Q623.88 of type=SNP alleles=[T*, C] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=-1.900, AS_FS=0.000, AS_MQ=55.21, AS_MQRankSum=1.000, AS_QD=20.80, AS_ReadPosRankSum=0.200, AS_SOR=0.998, BaseQRankSum=-1.821e+00, DP=66, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.250, MQ=53.72, MQRankSum=1.03, QD=20.80, RAW_MQ=86585.00, ReadPosRankSum=0.249, SOR=0.998} GT=GT:AD:DP:GQ:PGT:PID:PL 0/1:15,15:.:99:0|1:10433382_T_C:632,0,601 0/0:36,0:36:99:.:.:0,99,1182 filters=) 0.001s passed
testFinalizeAnnotationAgainstExpected[7]([[VC Unknown @ 20:10433391 Q602.77 of type=MIXED alleles=[T*, <NON_REF>, C] attr={AS_RAW_BaseQRankSum=[|-0.3, 1|NaN], AS_RAW_MQ=51662.00|52082.00|0.00, AS_RAW_MQRankSum=[|1.3, 1|NaN], AS_RAW_ReadPosRankSum=[|1.5, 1|NaN], AS_SB_TABLE=[14, 4|13, 3|0, 0], BaseQRankSum=-0.284, DP=34, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=1.329, RAW_MQ=103744.00, ReadPosRankSum=1.536} GT=GT:AD:GQ:PGT:PID:PL:SB 0/1:18,16,0:99:0|1:10433382_T_C:631,0,673,685,724,1409:14,4,13,3 filters=, [VC Unknown @ 20:10433363-10433423 Q. of type=SYMBOLIC alleles=[G*, <NON_REF>] attr={END=10433423} GT=GT:DP:GQ:MIN_DP:PL 0/0:39:99:36:0,99,1182 filters=], [VC Unknown @ 20:10433391 Q. of type=MIXED alleles=[T*, <NON_REF>, C] attr={AS_RAW_BaseQRankSum=[|-0.3, 1|], AS_RAW_MQ=51662.00|52082.00|0.00, AS_RAW_MQRankSum=[|1.3, 1|], AS_RAW_ReadPosRankSum=[|1.5, 1|], AS_SB_TABLE=[14, 4|13, 3|0, 0], BaseQRankSum=-2.840e-01, DP=70, ExcessHet=3.01, MQRankSum=1.33, RAW_MQ=103744.00, ReadPosRankSum=1.54} GT=GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:SB ./.:18,16,0:.:99:.:0|1:10433382_T_C:631,0,673,685,724,1409:14,4,13,3 ./.:.:39:99:36:.:.:0,99,1182,99,1182,1182 filters=, [VC Unknown @ 20:10433391 Q622.88 of type=SNP alleles=[T*, C] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=-0.300, AS_FS=0.000, AS_MQ=57.05, AS_MQRankSum=1.300, AS_QD=18.32, AS_ReadPosRankSum=1.500, AS_SOR=0.859, BaseQRankSum=-2.840e-01, DP=70, ExcessHet=3.0103, FS=0.000, MLEAC=1, MLEAF=0.250, MQ=55.24, MQRankSum=1.33, QD=18.32, RAW_MQ=103744.00, ReadPosRankSum=1.54, SOR=0.859} GT=GT:AD:DP:GQ:PGT:PID:PL 0/1:18,16:.:99:0|1:10433382_T_C:631,0,673 0/0:36,0:36:99:.:.:0,99,1182 filters=) 0s passed
testFinalizeAnnotationAgainstExpected[8]([[VC Unknown @ 20:10433468 Q624.77 of type=MIXED alleles=[T*, <NON_REF>, C] attr={AS_RAW_BaseQRankSum=[|-1.4, 1|NaN], AS_RAW_MQ=63049.00|69241.00|0.00, AS_RAW_MQRankSum=[|0.0, 1|NaN], AS_RAW_ReadPosRankSum=[|1.4, 1|NaN], AS_SB_TABLE=[13, 5|12, 8|0, 0], BaseQRankSum=-1.312, DP=38, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=0.076, RAW_MQ=132290.00, ReadPosRankSum=1.463} GT=GT:AD:GQ:PL:SB 0/1:18,20,0:99:653,0,572,707,633,1339:13,5,12,8 filters=, [VC Unknown @ 20:10433461-10433469 Q. of type=SYMBOLIC alleles=[T*, <NON_REF>] attr={END=10433469} GT=GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 filters=], [VC Unknown @ 20:10433468 Q. of type=MIXED alleles=[T*, <NON_REF>, C] attr={AS_RAW_BaseQRankSum=[|-1.4, 1|], AS_RAW_MQ=63049.00|69241.00|0.00, AS_RAW_MQRankSum=[|0.0, 1|], AS_RAW_ReadPosRankSum=[|1.4, 1|], AS_SB_TABLE=[13, 5|12, 8|0, 0], BaseQRankSum=-1.312e+00, DP=68, ExcessHet=3.01, MQRankSum=0.076, RAW_MQ=132290.00, ReadPosRankSum=1.46} GT=GT:AD:DP:GQ:MIN_DP:PL:SB ./.:18,20,0:.:99:.:653,0,572,707,633,1339:13,5,12,8 ./.:.:31:81:30:0,81,1215,81,1215,1215 filters=, [VC Unknown @ 20:10433468 Q644.88 of type=SNP alleles=[T*, C] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=-1.400, AS_FS=2.955, AS_MQ=58.84, AS_MQRankSum=0.000, AS_QD=16.97, AS_ReadPosRankSum=1.400, AS_SOR=0.324, BaseQRankSum=-1.312e+00, DP=68, ExcessHet=3.0103, FS=2.955, MLEAC=1, MLEAF=0.250, MQ=59.00, MQRankSum=0.076, QD=16.97, RAW_MQ=132290.00, ReadPosRankSum=1.46, SOR=0.324} GT=GT:AD:DP:GQ:PL 0/1:18,20:.:99:653,0,572 0/0:30,0:30:81:0,81,1215 filters=) 0.001s passed
testFinalizeAnnotationAgainstExpected[9]([[VC Unknown @ 20:10433560 Q966.77 of type=MIXED alleles=[C*, <NON_REF>, A] attr={AS_RAW_BaseQRankSum=[|3.4, 1|NaN], AS_RAW_MQ=111600.00|87769.00|0.00, AS_RAW_MQRankSum=[|-1.1, 1|NaN], AS_RAW_ReadPosRankSum=[|1.3, 1|NaN], AS_SB_TABLE=[30, 1|22, 3|0, 0], BaseQRankSum=3.497, DP=56, ExcessHet=3.0103, MLEAC=[1, 0], MLEAF=[0.500, 0.00], MQRankSum=-1.078, RAW_MQ=199369.00, ReadPosRankSum=1.376} GT=GT:AD:GQ:PGT:PID:PL:SB 0/1:31,25,0:99:0|1:10433560_C_A:995,0,3032,1092,3110,4202:30,1,22,3 filters=, [VC Unknown @ 20:10433505-10433707 Q. of type=SYMBOLIC alleles=[T*, <NON_REF>] attr={END=10433707} GT=GT:DP:GQ:MIN_DP:PL 0/0:51:99:39:0,99,1485 filters=], [VC Unknown @ 20:10433560 Q. of type=MIXED alleles=[C*, <NON_REF>, A] attr={AS_RAW_BaseQRankSum=[|3.4, 1|], AS_RAW_MQ=111600.00|87769.00|0.00, AS_RAW_MQRankSum=[|-1.1, 1|], AS_RAW_ReadPosRankSum=[|1.3, 1|], AS_SB_TABLE=[30, 1|22, 3|0, 0], BaseQRankSum=3.50, DP=95, ExcessHet=3.01, MQRankSum=-1.078e+00, RAW_MQ=199369.00, ReadPosRankSum=1.38} GT=GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:SB ./.:31,25,0:.:99:.:0|1:10433560_C_A:995,0,3032,1092,3110,4202:30,1,22,3 ./.:.:51:99:39:.:.:0,99,1485,99,1485,1485 filters=, [VC Unknown @ 20:10433560 Q986.88 of type=SNP alleles=[C*, A] attr={AC=1, AF=0.250, AN=4, AS_BaseQRankSum=3.400, AS_FS=5.027, AS_MQ=59.25, AS_MQRankSum=-1.100, AS_QD=17.63, AS_ReadPosRankSum=1.300, AS_SOR=0.129, BaseQRankSum=3.50, DP=95, ExcessHet=3.0103, FS=5.027, MLEAC=1, MLEAF=0.250, MQ=59.67, MQRankSum=-1.078e+00, QD=17.62, RAW_MQ=199369.00, ReadPosRankSum=1.38, SOR=0.129} GT=GT:AD:DP:GQ:PGT:PID:PL 0/1:31,25:.:99:0|1:10433560_C_A:995,0,3032 0/0:39,0:39:99:.:.:0,99,1485 filters=) 0.001s passed
testFinalizeAnnotations 0s passed

Standard error

21:26:09.544 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
21:26:09.544 DEBUG GenomeLocParser -  1 (16000 bp)
21:26:09.544 DEBUG GenomeLocParser -  2 (16000 bp)
21:26:09.544 DEBUG GenomeLocParser -  3 (16000 bp)
21:26:09.544 DEBUG GenomeLocParser -  4 (16000 bp)
21:26:09.546 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/NA12878.AS.chr20snippet.g.vcf
21:26:09.548 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/NA12892.AS.chr20snippet.g.vcf
21:26:09.549 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/CombineGVCFs.output.vcf
21:26:09.551 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/GenotypeGVCFs.output.vcf
21:26:09.559 DEBUG FeatureDataSource - Cache statistics for FeatureInput /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/GenotypeGVCFs.output.vcf:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/GenotypeGVCFs.output.vcf:
21:26:09.559 DEBUG FeatureCache - Cache hit rate  was 68.42% (13 out of 19 total queries)
21:26:09.559 DEBUG FeatureDataSource - Cache statistics for FeatureInput /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/CombineGVCFs.output.vcf:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/CombineGVCFs.output.vcf:
21:26:09.559 DEBUG FeatureCache - Cache hit rate  was 68.42% (13 out of 19 total queries)
21:26:09.559 DEBUG FeatureDataSource - Cache statistics for FeatureInput /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/NA12892.AS.chr20snippet.g.vcf:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/NA12892.AS.chr20snippet.g.vcf:
21:26:09.559 DEBUG FeatureCache - Cache hit rate  was 68.42% (13 out of 19 total queries)
21:26:09.559 DEBUG FeatureDataSource - Cache statistics for FeatureInput /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/NA12878.AS.chr20snippet.g.vcf:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/NA12878.AS.chr20snippet.g.vcf:
21:26:09.559 DEBUG FeatureCache - Cache hit rate  was 68.42% (13 out of 19 total queries)
21:26:09.559 WARN  ReferenceConfidenceVariantContextMerger - At least one attribute was found (MQRankSum) for which there is no corresponding header line
21:26:09.559 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 20:10087820 the annotation MLEAC=[0, 1, 0] was not a numerical value and was ignored
21:26:09.560 WARN  ReferenceConfidenceVariantContextMerger - Reducible annotation 'AS_RAW_ReadPosRankSum' detected, add -G StandardAnnotation -G AS_StandardAnnotation to the command to annotate in the final VC with this annotation.
21:26:09.560 WARN  ReferenceConfidenceVariantContextMerger - At least one attribute was found (RAW_MQ) for which there is no corresponding header line
21:26:09.560 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 20:10433312 the annotation AS_RAW_ReadPosRankSum=|NaN|NaN|NaN was not a numerical value and was ignored
21:26:09.560 WARN  ReferenceConfidenceVariantContextMerger - Reducible annotation 'AS_RAW_ReadPosRankSum' detected, add -G StandardAnnotation -G AS_StandardAnnotation to the command to annotate in the final VC with this annotation.
21:26:09.561 WARN  ReferenceConfidenceVariantContextMerger - At least one attribute was found (MQRankSum) for which there is no corresponding header line
21:26:09.561 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 20:10433322 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
21:26:09.561 WARN  ReferenceConfidenceVariantContextMerger - Reducible annotation 'AS_RAW_ReadPosRankSum' detected, add -G StandardAnnotation -G AS_StandardAnnotation to the command to annotate in the final VC with this annotation.
21:26:09.562 WARN  ReferenceConfidenceVariantContextMerger - At least one attribute was found (MQRankSum) for which there is no corresponding header line
21:26:09.562 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 20:10433324 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
21:26:09.562 WARN  ReferenceConfidenceVariantContextMerger - Reducible annotation 'AS_RAW_ReadPosRankSum' detected, add -G StandardAnnotation -G AS_StandardAnnotation to the command to annotate in the final VC with this annotation.
21:26:09.563 WARN  ReferenceConfidenceVariantContextMerger - At least one attribute was found (MQRankSum) for which there is no corresponding header line
21:26:09.563 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 20:10433326 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
21:26:09.563 WARN  ReferenceConfidenceVariantContextMerger - Reducible annotation 'AS_RAW_ReadPosRankSum' detected, add -G StandardAnnotation -G AS_StandardAnnotation to the command to annotate in the final VC with this annotation.
21:26:09.564 WARN  ReferenceConfidenceVariantContextMerger - At least one attribute was found (RAW_MQ) for which there is no corresponding header line
21:26:09.564 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 20:10433328 the annotation AS_RAW_ReadPosRankSum=|||||| was not a numerical value and was ignored
21:26:09.564 WARN  ReferenceConfidenceVariantContextMerger - Reducible annotation 'AS_RAW_ReadPosRankSum' detected, add -G StandardAnnotation -G AS_StandardAnnotation to the command to annotate in the final VC with this annotation.
21:26:09.564 WARN  ReferenceConfidenceVariantContextMerger - At least one attribute was found (MQRankSum) for which there is no corresponding header line
21:26:09.564 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 20:10433382 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
21:26:09.565 WARN  ReferenceConfidenceVariantContextMerger - Reducible annotation 'AS_RAW_ReadPosRankSum' detected, add -G StandardAnnotation -G AS_StandardAnnotation to the command to annotate in the final VC with this annotation.
21:26:09.565 WARN  ReferenceConfidenceVariantContextMerger - At least one attribute was found (MQRankSum) for which there is no corresponding header line
21:26:09.565 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 20:10433391 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
21:26:09.565 WARN  ReferenceConfidenceVariantContextMerger - Reducible annotation 'AS_RAW_ReadPosRankSum' detected, add -G StandardAnnotation -G AS_StandardAnnotation to the command to annotate in the final VC with this annotation.
21:26:09.566 WARN  ReferenceConfidenceVariantContextMerger - At least one attribute was found (MQRankSum) for which there is no corresponding header line
21:26:09.566 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 20:10433468 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
21:26:09.566 WARN  ReferenceConfidenceVariantContextMerger - Reducible annotation 'AS_RAW_ReadPosRankSum' detected, add -G StandardAnnotation -G AS_StandardAnnotation to the command to annotate in the final VC with this annotation.
21:26:09.566 WARN  ReferenceConfidenceVariantContextMerger - At least one attribute was found (MQRankSum) for which there is no corresponding header line
21:26:09.566 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 20:10433560 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
21:26:09.567 WARN  ReferenceConfidenceVariantContextMerger - Reducible annotation 'AS_RAW_ReadPosRankSum' detected, add -G StandardAnnotation -G AS_StandardAnnotation to the command to annotate in the final VC with this annotation.
21:26:09.567 WARN  ReferenceConfidenceVariantContextMerger - At least one attribute was found (MQRankSum) for which there is no corresponding header line
21:26:09.567 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 20:10433575 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
21:26:09.567 WARN  ReferenceConfidenceVariantContextMerger - Reducible annotation 'AS_RAW_ReadPosRankSum' detected, add -G StandardAnnotation -G AS_StandardAnnotation to the command to annotate in the final VC with this annotation.
21:26:09.568 WARN  ReferenceConfidenceVariantContextMerger - At least one attribute was found (MQRankSum) for which there is no corresponding header line
21:26:09.568 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 20:10433594 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
21:26:09.568 WARN  ReferenceConfidenceVariantContextMerger - Reducible annotation 'AS_RAW_ReadPosRankSum' detected, add -G StandardAnnotation -G AS_StandardAnnotation to the command to annotate in the final VC with this annotation.
21:26:09.569 WARN  ReferenceConfidenceVariantContextMerger - At least one attribute was found (MQRankSum) for which there is no corresponding header line
21:26:09.569 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 20:10433955 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
21:26:09.569 WARN  ReferenceConfidenceVariantContextMerger - Reducible annotation 'AS_RAW_ReadPosRankSum' detected, add -G StandardAnnotation -G AS_StandardAnnotation to the command to annotate in the final VC with this annotation.
21:26:09.569 WARN  ReferenceConfidenceVariantContextMerger - At least one attribute was found (MQRankSum) for which there is no corresponding header line
21:26:09.569 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 20:10434177 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
21:26:09.570 WARN  ReferenceConfidenceVariantContextMerger - Reducible annotation 'AS_RAW_ReadPosRankSum' detected, add -G StandardAnnotation -G AS_StandardAnnotation to the command to annotate in the final VC with this annotation.
21:26:09.570 WARN  ReferenceConfidenceVariantContextMerger - At least one attribute was found (MQRankSum) for which there is no corresponding header line
21:26:09.570 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 20:10434384 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
21:26:09.570 WARN  ReferenceConfidenceVariantContextMerger - Reducible annotation 'AS_RAW_ReadPosRankSum' detected, add -G StandardAnnotation -G AS_StandardAnnotation to the command to annotate in the final VC with this annotation.
21:26:09.571 WARN  ReferenceConfidenceVariantContextMerger - At least one attribute was found (MQRankSum) for which there is no corresponding header line
21:26:09.571 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 20:10435067 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
21:26:09.571 WARN  ReferenceConfidenceVariantContextMerger - Reducible annotation 'AS_RAW_ReadPosRankSum' detected, add -G StandardAnnotation -G AS_StandardAnnotation to the command to annotate in the final VC with this annotation.
21:26:09.571 WARN  ReferenceConfidenceVariantContextMerger - At least one attribute was found (MQRankSum) for which there is no corresponding header line
21:26:09.571 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 20:10434258 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
21:26:09.571 WARN  ReferenceConfidenceVariantContextMerger - Reducible annotation 'AS_RAW_ReadPosRankSum' detected, add -G StandardAnnotation -G AS_StandardAnnotation to the command to annotate in the final VC with this annotation.
21:26:09.572 WARN  ReferenceConfidenceVariantContextMerger - At least one attribute was found (MQRankSum) for which there is no corresponding header line
21:26:09.572 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 20:10436227 the annotation MLEAC=[1, 1, 0] was not a numerical value and was ignored
21:26:09.572 WARN  ReferenceConfidenceVariantContextMerger - Reducible annotation 'AS_RAW_ReadPosRankSum' detected, add -G StandardAnnotation -G AS_StandardAnnotation to the command to annotate in the final VC with this annotation.
21:26:09.573 WARN  ReferenceConfidenceVariantContextMerger - At least one attribute was found (RAW_MQ) for which there is no corresponding header line
21:26:09.573 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 20:10684106 the annotation AS_RAW_ReadPosRankSum=|NaN|NaN|NaN was not a numerical value and was ignored
21:26:09.573 WARN  ReferenceConfidenceVariantContextMerger - Reducible annotation 'AS_RAW_ReadPosRankSum' detected, add -G StandardAnnotation -G AS_StandardAnnotation to the command to annotate in the final VC with this annotation.
21:26:09.574 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/NA12878.AS.chr20snippet.g.vcf
21:26:09.575 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/NA12892.AS.chr20snippet.g.vcf
21:26:09.576 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/CombineGVCFs.output.vcf
21:26:09.578 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/GenotypeGVCFs.output.vcf
21:26:09.585 DEBUG FeatureDataSource - Cache statistics for FeatureInput /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/GenotypeGVCFs.output.vcf:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/GenotypeGVCFs.output.vcf:
21:26:09.585 DEBUG FeatureCache - Cache hit rate  was 68.42% (13 out of 19 total queries)
21:26:09.585 DEBUG FeatureDataSource - Cache statistics for FeatureInput /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/CombineGVCFs.output.vcf:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/CombineGVCFs.output.vcf:
21:26:09.585 DEBUG FeatureCache - Cache hit rate  was 68.42% (13 out of 19 total queries)
21:26:09.585 DEBUG FeatureDataSource - Cache statistics for FeatureInput /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/NA12892.AS.chr20snippet.g.vcf:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/NA12892.AS.chr20snippet.g.vcf:
21:26:09.585 DEBUG FeatureCache - Cache hit rate  was 68.42% (13 out of 19 total queries)
21:26:09.585 DEBUG FeatureDataSource - Cache statistics for FeatureInput /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/NA12878.AS.chr20snippet.g.vcf:/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/NA12878.AS.chr20snippet.g.vcf:
21:26:09.585 DEBUG FeatureCache - Cache hit rate  was 68.42% (13 out of 19 total queries)