Class org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.SystemCommandUtilsTest

all > org.broadinstitute.hellbender.tools.walkers.vqsr.scalable > SystemCommandUtilsTest

tests

failures

ignored

0.036s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testRunDiffException	0.032s	passed
testRunDiffIdenticalFile	0.002s	passed
testRunDiffNoSuchFile	0.002s	passed

Standard output

3372,3456c3372,4131
< chr1	943136	.	GA	G	.	.	training
< chr1	945259	.	TC	T	.	.	training
< chr1	965337	.	CTTAT	C	.	.	training
< chr1	1013466	.	T	TA	.	.	training
< chr1	1043223	.	CCT	C	.	.	training
< chr1	1063661	.	ATG	A	.	.	training
< chr1	1180460	.	AC	A	.	.	training
< chr1	1217383	.	AGCCGCG	A	.	.	training
< chr1	1223154	.	G	GAC	.	.	training
< chr1	1223182	.	AAC	A	.	.	training
< chr1	1228431	.	G	GGACA	.	.	training
< chr1	1242538	.	CT	C	.	.	training
< chr1	1255533	.	CT	C	.	.	training
< chr1	1299382	.	AG	A	.	.	training
< chr1	1331945	.	G	GC	.	.	training
< chr1	1353552	.	GCA	G	.	.	training
< chr1	1385919	.	A	AG	.	.	training
< chr1	1387763	.	CCT	C	.	.	training
< chr1	1398672	.	CTAGAG	C	.	.	training
< chr1	1400756	.	GGA	G	.	.	training
< chr1	1431026	.	CCACCCCCT	C	.	.	training
< chr1	1459283	.	AC	A	.	.	training
< chr1	1489578	.	C	CTA	.	.	training
< chr1	1541943	.	GCA	G	.	.	training
< chr1	1583446	.	C	CG	.	.	training
< chr1	1624323	.	AT	A	.	.	training
< chr1	1626527	.	TCGGGGC	T	.	.	training
< chr1	1716210	.	C	CT	.	.	training
< chr1	1721893	.	GT	G	.	.	training
< chr1	1955672	.	GC	G	.	.	training
< chr1	1968585	.	TG	T	.	.	training
< chr1	2025780	.	CG	C	.	.	training
< chr1	2028422	.	G	GC	.	.	training
< chr1	2596462	.	TG	T	.	.	training
< chr1	2598902	.	A	AG	.	.	training
< chr1	3021843	.	CAGA	C	.	.	training
< chr1	3479409	.	ACC	A	.	.	training
< chr1	3479714	.	T	TGCCCCG	.	.	training
< chr1	3493134	.	AG	A	.	.	training
< chr1	3625542	.	T	TG	.	.	training
< chr1	3627671	.	TA	T	.	.	training
< chr1	3629700	.	CCGGG	C	.	.	training
< chr1	3754088	.	TTGTC	T	.	.	training
< chr1	3756585	.	CAA	C	.	.	training
< chr1	3766519	.	TTC	T	.	.	training
< chr1	3780199	.	C	CAG	.	.	training
< chr1	3782574	.	GT	G	.	.	training
< chr1	3826260	.	TTA	T	.	.	training
< chr1	3847387	.	GA	G	.	.	training
< chr1	3852426	.	T	TTA	.	.	training
< chr1	3900023	.	GC	G	.	.	training
< chr1	3948113	.	AG	A	.	.	training
< chr1	4412094	.	TA	T	.	.	training
< chr1	4712522	.	GCCA	G	.	.	training
< chr1	4783223	.	AT	A	.	.	training
< chr1	4973625	.	TC	T	.	.	training
< chr1	5866521	.	TA	T	.	.	calibration
< chr1	5879457	.	CTTCT	C	.	.	calibration
< chr1	5880003	.	GCA	G	.	.	calibration
< chr1	5880031	.	GCA	G	.	.	calibration
< chr1	5886523	.	TTG	T	.	.	calibration
< chr1	6110364	.	CG	C	.	.	calibration
< chr1	6127984	.	TG	T	.	.	calibration
< chr1	6192905	.	CCA	C	.	.	calibration
< chr1	6327539	.	GT	G	.	.	calibration
< chr1	6466142	.	CCGTGCTCT	C	.	.	calibration
< chr1	6466180	.	GCGCC	G	.	.	calibration
< chr1	6524251	.	G	GTA	.	.	calibration
< chr1	6548233	.	CGCCT	C	.	.	calibration
< chr1	6549503	.	CAT	C	.	.	calibration
< chr1	6549732	.	G	GT	.	.	calibration
< chr1	6591390	.	CA	C	.	.	calibration
< chr1	7766608	.	TAC	T	.	.	calibration
< chr1	7801093	.	C	CT	.	.	calibration
< chr1	7803675	.	CTTA	C	.	.	calibration
< chr1	7847745	.	C	CT	.	.	calibration
< chr1	7969483	.	T	TC	.	.	calibration
< chr1	8192538	.	T	TA	.	.	calibration
< chr1	8364924	.	GA	G	.	.	calibration
< chr1	8866226	.	A	AG	.	.	calibration
< chr1	8949177	.	CCTGGCCT	C	.	.	calibration
< chr1	9244919	.	CCCCAGGCA	C	.	.	calibration
< chr1	9263404	.	C	CTGAGGCAG	.	.	calibration
< chr1	9265644	.	C	CT	.	.	calibration
< chr1	9717393	.	G	GGA	.	.	calibration
---
> chr1	629906	.	C	T	.	.	training
> chr1	847924	.	T	C	.	.	training
> chr1	874496	.	A	G	.	.	training
> chr1	914618	.	A	G	.	.	training
> chr1	917495	.	C	T	.	.	training
> chr1	917584	.	T	G	.	.	training
> chr1	919397	.	A	G	.	.	training
> chr1	930314	.	C	T	.	.	training
> chr1	935835	.	C	G	.	.	training
> chr1	943429	.	C	T	.	.	training
> chr1	943937	.	C	T	.	.	training
> chr1	944296	.	G	A	.	.	training
> chr1	944307	.	T	C	.	.	training
> chr1	944858	.	A	G	.	.	training
> chr1	946247	.	G	A	.	.	training
> chr1	946538	.	G	A	.	.	training
> chr1	946653	.	G	A	.	.	training
> chr1	952157	.	C	T	.	.	training
> chr1	952180	.	A	C	.	.	training
> chr1	952421	.	A	G	.	.	training
> chr1	953279	.	T	C	.	.	training
> chr1	959193	.	G	A	.	.	training
> chr1	961570	.	C	A	.	.	training
> chr1	961945	.	G	C	.	.	training
> chr1	962358	.	C	T	.	.	training
> chr1	965592	.	T	G	.	.	training
> chr1	973034	.	C	T	.	.	training
> chr1	973443	.	G	A	.	.	training
> chr1	973693	.	C	T	.	.	training
> chr1	973858	.	G	C	.	.	training
> chr1	975058	.	A	G	.	.	training
> chr1	976215	.	A	G	.	.	training
> chr1	976536	.	C	T	.	.	training
> chr1	979496	.	T	C	.	.	training
> chr1	979847	.	A	G	.	.	training
> chr1	981169	.	A	G	.	.	training
> chr1	981210	.	G	A	.	.	training
> chr1	1013312	.	G	A	.	.	training
> chr1	1014228	.	G	A	.	.	training
> chr1	1014274	.	A	G	.	.	training
> chr1	1022260	.	C	T	.	.	training
> chr1	1044368	.	A	T	.	.	training
> chr1	1047561	.	T	C	.	.	training
> chr1	1047614	.	T	C	.	.	training
> chr1	1048922	.	T	C	.	.	training
> chr1	1049886	.	C	T	.	.	training
> chr1	1050080	.	T	C	.	.	training
> chr1	1050520	.	C	T	.	.	training
> chr1	1051820	.	C	T	.	.	training
> chr1	1052290	.	T	G	.	.	training
> chr1	1054120	.	G	A	.	.	training
> chr1	1054900	.	C	T	.	.	training
> chr1	1055000	.	C	T	.	.	training
> chr1	1055037	.	T	C	.	.	training
> chr1	1055137	.	C	T	.	.	training
> chr1	1055604	.	G	A	.	.	training
> chr1	1063015	.	A	G	.	.	training
> chr1	1071610	.	G	A	.	.	training
> chr1	1071823	.	A	G	.	.	training
> chr1	1081817	.	C	T	.	.	training
> chr1	1083324	.	A	G	.	.	training
> chr1	1085966	.	A	G	.	.	training
> chr1	1086035	.	A	G	.	.	training
> chr1	1087765	.	G	A	.	.	training
> chr1	1091327	.	C	A	.	.	training
> chr1	1169204	.	T	C	.	.	training
> chr1	1174402	.	G	A	.	.	training
> chr1	1179830	.	G	A	.	.	training
> chr1	1180614	.	G	A	.	.	training
> chr1	1182832	.	T	C	.	.	training
> chr1	1182895	.	C	T	.	.	training
> chr1	1185051	.	G	A	.	.	training
> chr1	1185241	.	T	C	.	.	training
> chr1	1203533	.	T	C	.	.	training
> chr1	1212042	.	C	T	.	.	training
> chr1	1217733	.	G	A	.	.	training
> chr1	1220424	.	T	C	.	.	training
> chr1	1220751	.	T	C	.	.	training
> chr1	1223251	.	A	G	.	.	training
> chr1	1242865	.	C	T	.	.	training
> chr1	1243102	.	A	G	.	.	training
> chr1	1243545	.	G	A	.	.	training
> chr1	1244420	.	G	A	.	.	training
> chr1	1255143	.	C	T	.	.	training
> chr1	1257135	.	A	G	.	.	training
> chr1	1285758	.	G	A	.	.	training
> chr1	1286887	.	G	C	.	.	training
> chr1	1287310	.	C	T	.	.	training
> chr1	1290232	.	G	A	.	.	training
> chr1	1290261	.	C	A	.	.	training
> chr1	1290912	.	G	A	.	.	training
> chr1	1291310	.	C	T	.	.	training
> chr1	1291377	.	G	A	.	.	training
> chr1	1291869	.	T	C	.	.	training
> chr1	1296276	.	G	A	.	.	training
> chr1	1298561	.	T	C	.	.	training
> chr1	1303112	.	G	A	.	.	training
> chr1	1303959	.	T	G	.	.	training
> chr1	1304573	.	A	G	.	.	training
> chr1	1305337	.	T	C	.	.	training
> chr1	1310624	.	A	G	.	.	training
> chr1	1311058	.	G	A	.	.	training
> chr1	1312114	.	T	C	.	.	training
> chr1	1313807	.	G	A	.	.	training
> chr1	1319056	.	A	G	.	.	training
> chr1	1322866	.	A	C	.	.	training
> chr1	1327211	.	C	T	.	.	training
> chr1	1327764	.	G	A	.	.	training
> chr1	1334606	.	G	A	.	.	training
> chr1	1337736	.	A	G	.	.	training
> chr1	1342153	.	T	C	.	.	training
> chr1	1353443	.	A	G	.	.	training
> chr1	1373602	.	A	G	.	.	training
> chr1	1375544	.	T	C	.	.	training
> chr1	1378635	.	C	T	.	.	training
> chr1	1378792	.	C	T	.	.	training
> chr1	1378865	.	C	T	.	.	training
> chr1	1387698	.	A	G	.	.	training
> chr1	1393591	.	C	T	.	.	training
> chr1	1398218	.	C	A	.	.	training
> chr1	1400410	.	A	G	.	.	training
> chr1	1401954	.	G	T	.	.	training
> chr1	1426253	.	G	A	.	.	training
> chr1	1426261	.	C	T	.	.	training
> chr1	1460958	.	G	A	.	.	training
> chr1	1469429	.	A	G	.	.	training
> chr1	1489767	.	T	C	.	.	training
> chr1	1490122	.	A	G	.	.	training
> chr1	1490320	.	T	C	.	.	training
> chr1	1516000	.	T	C	.	.	training
> chr1	1523574	.	C	T	.	.	training
> chr1	1541728	.	G	A	.	.	training
> chr1	1541864	.	T	C	.	.	training
> chr1	1543953	.	A	G	.	.	training
> chr1	1563918	.	A	G	.	.	training
> chr1	1575421	.	C	T	.	.	training
> chr1	1583688	.	A	C	.	.	training
> chr1	1598344	.	C	T	.	.	training
> chr1	1613769	.	C	T	.	.	training
> chr1	1615322	.	A	G	.	.	training
> chr1	1616547	.	T	C	.	.	training
> chr1	1617375	.	T	C	.	.	training
> chr1	1618290	.	G	C	.	.	training
> chr1	1618982	.	G	A	.	.	training
> chr1	1623412	.	T	C	.	.	training
> chr1	1624086	.	G	A	.	.	training
> chr1	1624723	.	C	T	.	.	training
> chr1	1625951	.	G	A	.	.	training
> chr1	1627156	.	G	A	.	.	training
> chr1	1628409	.	C	A	.	.	training
> chr1	1628814	.	C	T	.	.	training
> chr1	1629332	.	G	T	.	.	training
> chr1	1665061	.	C	T	.	.	training
> chr1	1671148	.	C	T	.	.	training
> chr1	1671724	.	C	T	.	.	training
> chr1	1671995	.	G	T	.	.	training
> chr1	1731456	.	A	G	.	.	training
> chr1	1732392	.	C	T	.	.	training
> chr1	1732422	.	G	A	.	.	training
> chr1	1732580	.	T	C	.	.	training
> chr1	1732685	.	T	C	.	.	training
> chr1	1753033	.	C	T	.	.	training
> chr1	1754642	.	G	A	.	.	training
> chr1	1755504	.	T	C	.	.	training
> chr1	1756352	.	C	T	.	.	training
> chr1	1756945	.	G	A	.	.	training
> chr1	1759611	.	C	T	.	.	training
> chr1	1915143	.	A	G	.	.	training
> chr1	1915326	.	G	A	.	.	training
> chr1	1917295	.	A	G	.	.	training
> chr1	1918305	.	G	A	.	.	training
> chr1	1918484	.	C	A	.	.	training
> chr1	1918697	.	C	T	.	.	training
> chr1	1921955	.	T	C	.	.	training
> chr1	1922670	.	A	G	.	.	training
> chr1	1922882	.	A	G	.	.	training
> chr1	1923880	.	C	T	.	.	training
> chr1	1924659	.	C	T	.	.	training
> chr1	1927692	.	C	T	.	.	training
> chr1	1942186	.	G	A	.	.	training
> chr1	1947189	.	C	T	.	.	training
> chr1	1953616	.	C	T	.	.	training
> chr1	1955424	.	T	C	.	.	training
> chr1	1955580	.	A	G	.	.	training
> chr1	1955806	.	G	A	.	.	training
> chr1	1956754	.	C	A	.	.	training
> chr1	1956891	.	C	T	.	.	training
> chr1	1956930	.	A	G	.	.	training
> chr1	1959824	.	A	T	.	.	training
> chr1	1963738	.	C	T	.	.	training
> chr1	1964894	.	G	A	.	.	training
> chr1	1965001	.	G	A	.	.	training
> chr1	1965114	.	C	T	.	.	training
> chr1	1968747	.	T	C	.	.	training
> chr1	1968786	.	C	T	.	.	training
> chr1	1968793	.	T	C	.	.	training
> chr1	1985148	.	G	T	.	.	training
> chr1	1985367	.	C	T	.	.	training
> chr1	1985451	.	C	T	.	.	training
> chr1	1987049	.	A	G	.	.	training
> chr1	2024545	.	C	T	.	.	training
> chr1	2029235	.	C	T	.	.	training
> chr1	2030027	.	C	T	.	.	training
> chr1	2056364	.	G	A	.	.	training
> chr1	2056554	.	T	C	.	.	training
> chr1	2059575	.	A	G	.	.	training
> chr1	2074301	.	T	C	.	.	training
> chr1	2075289	.	T	C	.	.	training
> chr1	2104824	.	G	A	.	.	training
> chr1	2111641	.	T	G	.	.	training
> chr1	2142665	.	G	T	.	.	training
> chr1	2144131	.	T	C	.	.	training
> chr1	2151019	.	C	T	.	.	training
> chr1	2151066	.	C	T	.	.	training
> chr1	2151127	.	T	C	.	.	training
> chr1	2156118	.	T	C	.	.	training
> chr1	2181827	.	G	A	.	.	training
> chr1	2186119	.	C	T	.	.	training
> chr1	2186900	.	A	G	.	.	training
> chr1	2186920	.	A	G	.	.	training
> chr1	2189679	.	C	T	.	.	training
> chr1	2212668	.	A	G	.	.	training
> chr1	2213349	.	A	G	.	.	training
> chr1	2229060	.	C	T	.	.	training
> chr1	2303193	.	G	A	.	.	training
> chr1	2303580	.	T	C	.	.	training
> chr1	2304223	.	G	A	.	.	training
> chr1	2304233	.	C	T	.	.	training
> chr1	2306798	.	A	T	.	.	training
> chr1	2321320	.	A	G	.	.	training
> chr1	2326424	.	C	T	.	.	training
> chr1	2332449	.	C	T	.	.	training
> chr1	2351551	.	C	T	.	.	training
> chr1	2351678	.	C	T	.	.	training
> chr1	2351827	.	T	C	.	.	training
> chr1	2351874	.	C	G	.	.	training
> chr1	2352756	.	T	C	.	.	training
> chr1	2371472	.	G	A	.	.	training
> chr1	2372127	.	A	G	.	.	training
> chr1	2374713	.	C	T	.	.	training
> chr1	2375256	.	C	T	.	.	training
> chr1	2375471	.	C	T	.	.	training
> chr1	2375533	.	G	A	.	.	training
> chr1	2377643	.	T	G	.	.	training
> chr1	2384876	.	A	G	.	.	training
> chr1	2385630	.	A	C	.	.	training
> chr1	2387214	.	G	A	.	.	training
> chr1	2387989	.	A	G	.	.	training
> chr1	2394570	.	G	A	.	.	training
> chr1	2395636	.	C	T	.	.	training
> chr1	2396376	.	C	T	.	.	training
> chr1	2397275	.	A	G	.	.	training
> chr1	2404237	.	A	G	.	.	training
> chr1	2405593	.	C	T	.	.	training
> chr1	2405755	.	C	T	.	.	training
> chr1	2408761	.	T	C	.	.	training
> chr1	2408773	.	G	A	.	.	training
> chr1	2430201	.	G	T	.	.	training
> chr1	2480012	.	A	G	.	.	training
> chr1	2487186	.	C	T	.	.	training
> chr1	2489151	.	T	C	.	.	training
> chr1	2489474	.	A	G	.	.	training
> chr1	2493326	.	G	A	.	.	training
> chr1	2494553	.	C	T	.	.	training
> chr1	2499178	.	C	T	.	.	training
> chr1	2499618	.	C	T	.	.	training
> chr1	2512975	.	G	A	.	.	training
> chr1	2513031	.	C	T	.	.	training
> chr1	2513967	.	A	G	.	.	training
> chr1	2520882	.	C	T	.	.	training
> chr1	2520918	.	G	A	.	.	training
> chr1	2521005	.	A	G	.	.	training
> chr1	2556224	.	C	A	.	.	training
> chr1	2556327	.	T	C	.	.	training
> chr1	2556714	.	A	G	.	.	training
> chr1	2559503	.	C	A	.	.	training
> chr1	2562891	.	G	A	.	.	training
> chr1	2563346	.	G	A	.	.	training
> chr1	2566588	.	A	G	.	.	training
> chr1	2589991	.	C	T	.	.	training
> chr1	2590765	.	G	T	.	.	training
> chr1	2590953	.	G	A	.	.	training
> chr1	2595307	.	A	G	.	.	training
> chr1	2596694	.	T	C	.	.	training
> chr1	2605633	.	C	T	.	.	training
> chr1	2609830	.	A	G	.	.	training
> chr1	2632744	.	T	C	.	.	training
> chr1	2641760	.	A	G	.	.	training
> chr1	2783827	.	C	T	.	.	training
> chr1	3021701	.	C	T	.	.	training
> chr1	3022133	.	T	G	.	.	training
> chr1	3022360	.	T	G	.	.	training
> chr1	3022425	.	G	A	.	.	training
> chr1	3022845	.	G	T	.	.	training
> chr1	3060252	.	T	C	.	.	training
> chr1	3064014	.	C	T	.	.	training
> chr1	3067399	.	G	A	.	.	training
> chr1	3067523	.	C	A	.	.	training
> chr1	3133009	.	C	T	.	.	training
> chr1	3133149	.	G	A	.	.	training
> chr1	3309376	.	C	T	.	.	training
> chr1	3385157	.	C	T	.	.	training
> chr1	3386882	.	T	C	.	.	training
> chr1	3396350	.	T	G	.	.	training
> chr1	3411241	.	C	T	.	.	training
> chr1	3411794	.	T	C	.	.	training
> chr1	3412095	.	C	T	.	.	training
> chr1	3412820	.	C	T	.	.	training
> chr1	3425966	.	G	A	.	.	training
> chr1	3426240	.	G	T	.	.	training
> chr1	3435783	.	T	C	.	.	training
> chr1	3435977	.	T	C	.	.	training
> chr1	3436015	.	T	C	.	.	training
> chr1	3437326	.	A	G	.	.	training
> chr1	3437385	.	A	G	.	.	training
> chr1	3467101	.	G	A	.	.	training
> chr1	3467334	.	A	G	.	.	training
> chr1	3468565	.	G	A	.	.	training
> chr1	3468692	.	A	G	.	.	training
> chr1	3471842	.	A	G	.	.	training
> chr1	3472757	.	C	T	.	.	training
> chr1	3477892	.	T	C	.	.	training
> chr1	3478475	.	G	A	.	.	training
> chr1	3478610	.	C	A	.	.	training
> chr1	3480498	.	G	A	.	.	training
> chr1	3480624	.	T	C	.	.	training
> chr1	3481000	.	C	T	.	.	training
> chr1	3490227	.	A	G	.	.	training
> chr1	3490443	.	G	A	.	.	training
> chr1	3490479	.	G	T	.	.	training
> chr1	3493741	.	C	T	.	.	training
> chr1	3494409	.	C	T	.	.	training
> chr1	3496080	.	G	A	.	.	training
> chr1	3497433	.	G	A	.	.	training
> chr1	3499885	.	C	A	.	.	training
> chr1	3499938	.	C	T	.	.	training
> chr1	3505333	.	A	G	.	.	training
> chr1	3506078	.	A	G	.	.	training
> chr1	3507824	.	G	A	.	.	training
> chr1	3508619	.	G	A	.	.	training
> chr1	3510030	.	A	G	.	.	training
> chr1	3510787	.	A	G	.	.	training
> chr1	3511596	.	T	G	.	.	training
> chr1	3512044	.	G	A	.	.	training
> chr1	3524260	.	G	A	.	.	training
> chr1	3579915	.	T	C	.	.	training
> chr1	3595370	.	A	G	.	.	training
> chr1	3602380	.	T	C	.	.	training
> chr1	3627782	.	T	C	.	.	training
> chr1	3628686	.	T	G	.	.	training
> chr1	3631778	.	G	A	.	.	training
> chr1	3632268	.	G	C	.	.	training
> chr1	3633288	.	G	A	.	.	training
> chr1	3635228	.	G	A	.	.	training
> chr1	3650142	.	G	A	.	.	training
> chr1	3682346	.	C	T	.	.	training
> chr1	3682950	.	C	T	.	.	training
> chr1	3712099	.	A	G	.	.	training
> chr1	3712113	.	A	G	.	.	training
> chr1	3722110	.	C	T	.	.	training
> chr1	3727363	.	A	G	.	.	training
> chr1	3728190	.	T	C	.	.	training
> chr1	3729425	.	G	A	.	.	training
> chr1	3729573	.	C	T	.	.	training
> chr1	3729727	.	G	A	.	.	training
> chr1	3731398	.	T	C	.	.	training
> chr1	3732839	.	G	A	.	.	training
> chr1	3732857	.	T	C	.	.	training
> chr1	3732998	.	G	A	.	.	training
> chr1	3734562	.	G	T	.	.	training
> chr1	3734754	.	A	G	.	.	training
> chr1	3736848	.	A	C	.	.	training
> chr1	3736862	.	T	C	.	.	training
> chr1	3741195	.	G	A	.	.	training
> chr1	3743178	.	C	T	.	.	training
> chr1	3746281	.	A	G	.	.	training
> chr1	3746564	.	G	A	.	.	training
> chr1	3751440	.	T	C	.	.	training
> chr1	3752637	.	A	G	.	.	training
> chr1	3761369	.	T	C	.	.	training
> chr1	3762582	.	G	A	.	.	training
> chr1	3763211	.	C	T	.	.	training
> chr1	3771466	.	C	G	.	.	training
> chr1	3772844	.	G	A	.	.	training
> chr1	3775163	.	A	C	.	.	training
> chr1	3781099	.	C	T	.	.	training
> chr1	3781136	.	G	A	.	.	training
> chr1	3783652	.	C	T	.	.	training
> chr1	3785099	.	T	C	.	.	training
> chr1	3786773	.	G	C	.	.	training
> chr1	3787146	.	G	A	.	.	training
> chr1	3787339	.	C	T	.	.	training
> chr1	3815395	.	C	T	.	.	training
> chr1	3816032	.	G	T	.	.	training
> chr1	3825693	.	C	T	.	.	training
> chr1	3826755	.	G	A	.	.	training
> chr1	3829360	.	G	A	.	.	training
> chr1	3831016	.	C	T	.	.	training
> chr1	3834122	.	C	T	.	.	training
> chr1	3837249	.	T	C	.	.	training
> chr1	3839111	.	T	C	.	.	training
> chr1	3844915	.	C	T	.	.	training
> chr1	3848860	.	G	T	.	.	training
> chr1	3852155	.	T	C	.	.	training
> chr1	3857154	.	A	G	.	.	training
> chr1	3857574	.	T	C	.	.	training
> chr1	3867890	.	T	C	.	.	training
> chr1	3867900	.	G	A	.	.	training
> chr1	3869625	.	G	A	.	.	training
> chr1	3869681	.	G	A	.	.	training
> chr1	3873250	.	A	C	.	.	training
> chr1	3883678	.	A	G	.	.	training
> chr1	3889771	.	G	T	.	.	training
> chr1	3889794	.	T	C	.	.	training
> chr1	3890694	.	G	C	.	.	training
> chr1	3890824	.	G	A	.	.	training
> chr1	3890886	.	C	A	.	.	training
> chr1	3891029	.	G	C	.	.	training
> chr1	3891798	.	G	A	.	.	training
> chr1	3916629	.	C	T	.	.	training
> chr1	3944753	.	T	C	.	.	training
> chr1	3944985	.	G	T	.	.	training
> chr1	3946328	.	C	A	.	.	training
> chr1	3949011	.	T	C	.	.	training
> chr1	3955322	.	C	T	.	.	training
> chr1	3976135	.	T	C	.	.	training
> chr1	3995567	.	T	C	.	.	training
> chr1	4018388	.	G	A	.	.	training
> chr1	4175623	.	C	T	.	.	training
> chr1	4480984	.	A	G	.	.	training
> chr1	4481490	.	G	A	.	.	training
> chr1	4484118	.	T	C	.	.	training
> chr1	4572500	.	A	G	.	.	training
> chr1	4593033	.	C	T	.	.	training
> chr1	4593910	.	A	G	.	.	training
> chr1	4711993	.	T	C	.	.	training
> chr1	4712656	.	C	T	.	.	training
> chr1	4712657	.	G	A	.	.	training
> chr1	4769735	.	C	T	.	.	training
> chr1	4774546	.	T	C	.	.	training
> chr1	4785208	.	T	G	.	.	training
> chr1	4789324	.	T	C	.	.	training
> chr1	4790763	.	T	C	.	.	training
> chr1	4791243	.	A	G	.	.	training
> chr1	5090706	.	A	G	.	.	calibration
> chr1	5307372	.	A	G	.	.	calibration
> chr1	5480747	.	A	C	.	.	calibration
> chr1	5481145	.	C	A	.	.	calibration
> chr1	5481957	.	G	A	.	.	calibration
> chr1	5493410	.	T	C	.	.	calibration
> chr1	5493989	.	A	G	.	.	calibration
> chr1	5863309	.	C	T	.	.	calibration
> chr1	5863728	.	T	G	.	.	calibration
> chr1	5864686	.	T	C	.	.	calibration
> chr1	5864821	.	G	A	.	.	calibration
> chr1	5865311	.	G	A	.	.	calibration
> chr1	5866447	.	T	C	.	.	calibration
> chr1	5867678	.	G	A	.	.	calibration
> chr1	5873470	.	A	G	.	.	calibration
> chr1	5874430	.	A	G	.	.	calibration
> chr1	5874440	.	T	C	.	.	calibration
> chr1	5874777	.	C	T	.	.	calibration
> chr1	5875162	.	T	C	.	.	calibration
> chr1	5877031	.	T	C	.	.	calibration
> chr1	5877108	.	G	A	.	.	calibration
> chr1	5877267	.	C	T	.	.	calibration
> chr1	5882687	.	A	G	.	.	calibration
> chr1	5890953	.	C	T	.	.	calibration
> chr1	5905321	.	C	T	.	.	calibration
> chr1	5909185	.	G	A	.	.	calibration
> chr1	5927918	.	A	G	.	.	calibration
> chr1	5967192	.	A	G	.	.	calibration
> chr1	5986204	.	G	A	.	.	calibration
> chr1	6007580	.	C	G	.	.	calibration
> chr1	6040795	.	G	A	.	.	calibration
> chr1	6082379	.	C	T	.	.	calibration
> chr1	6085347	.	G	A	.	.	calibration
> chr1	6086101	.	C	G	.	.	calibration
> chr1	6088862	.	G	C	.	.	calibration
> chr1	6089062	.	G	A	.	.	calibration
> chr1	6090577	.	C	T	.	.	calibration
> chr1	6094357	.	C	T	.	.	calibration
> chr1	6097237	.	T	C	.	.	calibration
> chr1	6097374	.	C	T	.	.	calibration
> chr1	6098502	.	A	G	.	.	calibration
> chr1	6098972	.	A	G	.	.	calibration
> chr1	6102523	.	G	A	.	.	calibration
> chr1	6103081	.	C	T	.	.	calibration
> chr1	6103524	.	C	T	.	.	calibration
> chr1	6103865	.	C	T	.	.	calibration
> chr1	6110293	.	C	T	.	.	calibration
> chr1	6110639	.	C	G	.	.	calibration
> chr1	6111932	.	C	A	.	.	calibration
> chr1	6112780	.	C	T	.	.	calibration
> chr1	6123866	.	T	C	.	.	calibration
> chr1	6124032	.	A	G	.	.	calibration
> chr1	6124132	.	A	G	.	.	calibration
> chr1	6125004	.	G	A	.	.	calibration
> chr1	6127026	.	C	T	.	.	calibration
> chr1	6128486	.	G	A	.	.	calibration
> chr1	6130155	.	C	T	.	.	calibration
> chr1	6130255	.	C	T	.	.	calibration
> chr1	6131572	.	C	T	.	.	calibration
> chr1	6134346	.	T	C	.	.	calibration
> chr1	6135488	.	C	T	.	.	calibration
> chr1	6136809	.	A	G	.	.	calibration
> chr1	6142185	.	G	A	.	.	calibration
> chr1	6144101	.	G	A	.	.	calibration
> chr1	6144206	.	A	G	.	.	calibration
> chr1	6146689	.	A	G	.	.	calibration
> chr1	6150948	.	G	A	.	.	calibration
> chr1	6151123	.	G	A	.	.	calibration
> chr1	6152296	.	G	A	.	.	calibration
> chr1	6159303	.	G	T	.	.	calibration
> chr1	6192847	.	G	A	.	.	calibration
> chr1	6197766	.	T	C	.	.	calibration
> chr1	6197796	.	G	A	.	.	calibration
> chr1	6198087	.	C	T	.	.	calibration
> chr1	6208961	.	C	T	.	.	calibration
> chr1	6209280	.	A	G	.	.	calibration
> chr1	6211065	.	A	G	.	.	calibration
> chr1	6212753	.	C	T	.	.	calibration
> chr1	6213146	.	C	T	.	.	calibration
> chr1	6218354	.	A	G	.	.	calibration
> chr1	6219140	.	C	T	.	.	calibration
> chr1	6219310	.	G	C	.	.	calibration
> chr1	6219502	.	T	G	.	.	calibration
> chr1	6221607	.	A	C	.	.	calibration
> chr1	6225398	.	T	C	.	.	calibration
> chr1	6231750	.	A	G	.	.	calibration
> chr1	6244993	.	C	T	.	.	calibration
> chr1	6245243	.	C	A	.	.	calibration
> chr1	6248635	.	A	G	.	.	calibration
> chr1	6254419	.	C	T	.	.	calibration
> chr1	6254762	.	T	C	.	.	calibration
> chr1	6264553	.	C	T	.	.	calibration
> chr1	6327216	.	G	A	.	.	calibration
> chr1	6339720	.	A	G	.	.	calibration
> chr1	6416226	.	T	C	.	.	calibration
> chr1	6459964	.	C	A	.	.	calibration
> chr1	6460252	.	C	T	.	.	calibration
> chr1	6461090	.	A	C	.	.	calibration
> chr1	6464441	.	T	C	.	.	calibration
> chr1	6464628	.	T	C	.	.	calibration
> chr1	6465197	.	C	T	.	.	calibration
> chr1	6465948	.	A	G	.	.	calibration
> chr1	6467273	.	A	G	.	.	calibration
> chr1	6467536	.	A	G	.	.	calibration
> chr1	6469383	.	A	G	.	.	calibration
> chr1	6469747	.	C	T	.	.	calibration
> chr1	6470375	.	A	G	.	.	calibration
> chr1	6471064	.	T	C	.	.	calibration
> chr1	6471590	.	C	T	.	.	calibration
> chr1	6473333	.	G	C	.	.	calibration
> chr1	6474721	.	G	A	.	.	calibration
> chr1	6519461	.	G	C	.	.	calibration
> chr1	6519547	.	C	T	.	.	calibration
> chr1	6519783	.	C	T	.	.	calibration
> chr1	6525479	.	C	T	.	.	calibration
> chr1	6525744	.	C	T	.	.	calibration
> chr1	6532317	.	A	G	.	.	calibration
> chr1	6545037	.	T	C	.	.	calibration
> chr1	6549836	.	G	A	.	.	calibration
> chr1	6554475	.	G	A	.	.	calibration
> chr1	6555047	.	C	A	.	.	calibration
> chr1	6575171	.	A	G	.	.	calibration
> chr1	6575246	.	G	A	.	.	calibration
> chr1	6576996	.	G	A	.	.	calibration
> chr1	6579787	.	G	T	.	.	calibration
> chr1	6580056	.	A	G	.	.	calibration
> chr1	6580601	.	C	T	.	.	calibration
> chr1	6589168	.	T	G	.	.	calibration
> chr1	6589217	.	T	C	.	.	calibration
> chr1	6599445	.	G	A	.	.	calibration
> chr1	6599812	.	A	G	.	.	calibration
> chr1	6601672	.	C	A	.	.	calibration
> chr1	6601921	.	G	A	.	.	calibration
> chr1	6602853	.	G	A	.	.	calibration
> chr1	6617004	.	A	G	.	.	calibration
> chr1	6619788	.	C	T	.	.	calibration
> chr1	6621684	.	C	T	.	.	calibration
> chr1	6628298	.	G	A	.	.	calibration
> chr1	6629764	.	A	G	.	.	calibration
> chr1	6634147	.	A	G	.	.	calibration
> chr1	6634453	.	G	T	.	.	calibration
> chr1	6634514	.	G	A	.	.	calibration
> chr1	6634867	.	C	T	.	.	calibration
> chr1	6634920	.	G	A	.	.	calibration
> chr1	6635063	.	C	T	.	.	calibration
> chr1	6635184	.	A	G	.	.	calibration
> chr1	6635271	.	G	T	.	.	calibration
> chr1	6644575	.	A	G	.	.	calibration
> chr1	6645884	.	C	T	.	.	calibration
> chr1	6652712	.	C	T	.	.	calibration
> chr1	6653054	.	C	T	.	.	calibration
> chr1	6768548	.	A	G	.	.	calibration
> chr1	6806918	.	G	A	.	.	calibration
> chr1	7142130	.	T	C	.	.	calibration
> chr1	7441000	.	C	T	.	.	calibration
> chr1	7467936	.	T	C	.	.	calibration
> chr1	7640614	.	C	T	.	.	calibration
> chr1	7663474	.	G	A	.	.	calibration
> chr1	7663528	.	C	T	.	.	calibration
> chr1	7663897	.	G	A	.	.	calibration
> chr1	7700673	.	T	G	.	.	calibration
> chr1	7700832	.	A	G	.	.	calibration
> chr1	7732351	.	C	T	.	.	calibration
> chr1	7736581	.	A	G	.	.	calibration
> chr1	7737290	.	C	T	.	.	calibration
> chr1	7737443	.	C	G	.	.	calibration
> chr1	7745148	.	G	T	.	.	calibration
> chr1	7747853	.	A	G	.	.	calibration
> chr1	7752338	.	A	G	.	.	calibration
> chr1	7755494	.	G	A	.	.	calibration
> chr1	7771292	.	C	A	.	.	calibration
> chr1	7778053	.	A	C	.	.	calibration
> chr1	7785635	.	T	C	.	.	calibration
> chr1	7788497	.	G	A	.	.	calibration
> chr1	7803233	.	C	T	.	.	calibration
> chr1	7809988	.	T	C	.	.	calibration
> chr1	7810084	.	A	C	.	.	calibration
> chr1	7819262	.	C	T	.	.	calibration
> chr1	7819567	.	C	T	.	.	calibration
> chr1	7820623	.	T	G	.	.	calibration
> chr1	7827433	.	T	C	.	.	calibration
> chr1	7827545	.	G	A	.	.	calibration
> chr1	7829881	.	C	T	.	.	calibration
> chr1	7830204	.	A	G	.	.	calibration
> chr1	7837073	.	A	G	.	.	calibration
> chr1	7837168	.	G	A	.	.	calibration
> chr1	7844187	.	C	T	.	.	calibration
> chr1	7844415	.	G	A	.	.	calibration
> chr1	7847924	.	A	G	.	.	calibration
> chr1	7849677	.	C	T	.	.	calibration
> chr1	7851039	.	C	T	.	.	calibration
> chr1	7852944	.	A	G	.	.	calibration
> chr1	7853370	.	G	A	.	.	calibration
> chr1	7853385	.	C	T	.	.	calibration
> chr1	7853530	.	C	T	.	.	calibration
> chr1	7934909	.	G	A	.	.	calibration
> chr1	7938903	.	T	G	.	.	calibration
> chr1	7962764	.	C	T	.	.	calibration
> chr1	8015560	.	T	C	.	.	calibration
> chr1	8208655	.	T	C	.	.	calibration
> chr1	8292338	.	T	C	.	.	calibration
> chr1	8292344	.	G	A	.	.	calibration
> chr1	8325764	.	G	A	.	.	calibration
> chr1	8325939	.	C	T	.	.	calibration
> chr1	8329991	.	G	A	.	.	calibration
> chr1	8330153	.	G	A	.	.	calibration
> chr1	8330324	.	G	C	.	.	calibration
> chr1	8330828	.	G	A	.	.	calibration
> chr1	8335381	.	T	C	.	.	calibration
> chr1	8335500	.	G	T	.	.	calibration
> chr1	8337743	.	C	T	.	.	calibration
> chr1	8344033	.	C	T	.	.	calibration
> chr1	8353257	.	A	C	.	.	calibration
> chr1	8355175	.	C	T	.	.	calibration
> chr1	8358159	.	C	T	.	.	calibration
> chr1	8358584	.	C	A	.	.	calibration
> chr1	8358650	.	G	A	.	.	calibration
> chr1	8361032	.	C	T	.	.	calibration
> chr1	8362616	.	T	C	.	.	calibration
> chr1	8365840	.	T	C	.	.	calibration
> chr1	8466082	.	G	A	.	.	calibration
> chr1	8866693	.	T	C	.	.	calibration
> chr1	8945798	.	A	G	.	.	calibration
> chr1	8945916	.	G	A	.	.	calibration
> chr1	8949347	.	C	T	.	.	calibration
> chr1	8949385	.	A	C	.	.	calibration
> chr1	8949411	.	G	C	.	.	calibration
> chr1	8949488	.	C	A	.	.	calibration
> chr1	8951362	.	A	G	.	.	calibration
> chr1	8951478	.	G	A	.	.	calibration
> chr1	8951527	.	T	G	.	.	calibration
> chr1	8957032	.	C	T	.	.	calibration
> chr1	8957145	.	A	G	.	.	calibration
> chr1	8958872	.	A	G	.	.	calibration
> chr1	8967768	.	C	T	.	.	calibration
> chr1	8967840	.	G	T	.	.	calibration
> chr1	8970905	.	C	T	.	.	calibration
> chr1	8974242	.	T	C	.	.	calibration
> chr1	8974362	.	G	A	.	.	calibration
> chr1	8974539	.	A	G	.	.	calibration
> chr1	9003179	.	G	A	.	.	calibration
> chr1	9003206	.	C	T	.	.	calibration
> chr1	9007281	.	C	T	.	.	calibration
> chr1	9013742	.	C	T	.	.	calibration
> chr1	9014802	.	C	T	.	.	calibration
> chr1	9019095	.	C	T	.	.	calibration
> chr1	9019242	.	C	T	.	.	calibration
> chr1	9019306	.	G	A	.	.	calibration
> chr1	9024865	.	T	C	.	.	calibration
> chr1	9025220	.	C	T	.	.	calibration
> chr1	9035551	.	T	C	.	.	calibration
> chr1	9037182	.	C	T	.	.	calibration
> chr1	9037192	.	A	G	.	.	calibration
> chr1	9038171	.	C	T	.	.	calibration
> chr1	9039696	.	G	A	.	.	calibration
> chr1	9040420	.	G	A	.	.	calibration
> chr1	9047512	.	C	T	.	.	calibration
> chr1	9047790	.	G	T	.	.	calibration
> chr1	9057689	.	T	C	.	.	calibration
> chr1	9069561	.	C	T	.	.	calibration
> chr1	9069808	.	G	A	.	.	calibration
> chr1	9069886	.	A	G	.	.	calibration
> chr1	9072997	.	T	C	.	.	calibration
> chr1	9084954	.	T	C	.	.	calibration
> chr1	9101560	.	C	T	.	.	calibration
> chr1	9104074	.	G	A	.	.	calibration
> chr1	9104141	.	G	A	.	.	calibration
> chr1	9105610	.	G	A	.	.	calibration
> chr1	9105759	.	C	A	.	.	calibration
> chr1	9128817	.	T	C	.	.	calibration
> chr1	9180545	.	C	T	.	.	calibration
> chr1	9183752	.	G	T	.	.	calibration
> chr1	9196141	.	G	A	.	.	calibration
> chr1	9245386	.	A	C	.	.	calibration
> chr1	9246974	.	G	A	.	.	calibration
> chr1	9247079	.	T	C	.	.	calibration
> chr1	9263851	.	G	A	.	.	calibration
> chr1	9264154	.	C	T	.	.	calibration
> chr1	9264512	.	T	C	.	.	calibration
> chr1	9264611	.	A	G	.	.	calibration
> chr1	9265026	.	G	T	.	.	calibration
> chr1	9265206	.	C	T	.	.	calibration
> chr1	9265286	.	G	A	.	.	calibration
> chr1	9267328	.	T	G	.	.	calibration
> chr1	9355668	.	G	A	.	.	calibration
> chr1	9355751	.	G	A	.	.	calibration
> chr1	9356092	.	G	A	.	.	calibration
> chr1	9367783	.	A	G	.	.	calibration
> chr1	9367810	.	G	A	.	.	calibration
> chr1	9422389	.	G	A	.	.	calibration
> chr1	9503256	.	C	G	.	.	calibration
> chr1	9553813	.	C	T	.	.	calibration
> chr1	9582366	.	G	C	.	.	calibration
> chr1	9595907	.	C	T	.	.	calibration
> chr1	9598649	.	G	A	.	.	calibration
> chr1	9598751	.	A	G	.	.	calibration
> chr1	9653442	.	G	A	.	.	calibration
> chr1	9654189	.	A	G	.	.	calibration
> chr1	9654307	.	G	A	.	.	calibration
> chr1	9688387	.	T	G	.	.	calibration
> chr1	9716281	.	A	G	.	.	calibration
> chr1	9717471	.	A	G	.	.	calibration
> chr1	9717541	.	C	G	.	.	calibration
> chr1	9719813	.	T	C	.	.	calibration
> chr1	9722498	.	C	T	.	.	calibration
> chr1	9722708	.	C	T	.	.	calibration
> chr1	9727450	.	T	C	.	.	calibration
> chr1	9741283	.	G	A	.	.	calibration
> chr1	9744635	.	C	T	.	.	calibration
> chr1	9751377	.	A	G	.	.	calibration
> chr1	9751483	.	A	G	.	.	calibration
> chr1	9828144	.	C	T	.	.	calibration
> chr1	9850300	.	T	C	.	.	calibration
> chr1	9930054	.	A	G	.	.	calibration
> chr1	9936649	.	C	T	.	.	calibration
> chr1	9943262	.	G	A	.	.	calibration

Standard error

diff: /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/extract/expected/blahblah: No such file or directory