| samocha_enrichment_background |
enrichment/samocha_background
|
0 |
4 |
1.38 MB |
Samocha's Enrichment Background Model
|
| gene_score |
gene_properties/gene_scores/Iossifov_Wigler_PNAS_2015
|
0 |
6 |
7.8 MB |
Probability of a gene to be associated with autism
|
| gene_score |
gene_properties/gene_scores/LGD
|
0 |
7 |
544.15 KB |
Gene vulnerability/intolerance score based on the rare LGD variants
|
| gene_score |
gene_properties/gene_scores/LOEUF
|
0 |
9 |
13.19 MB |
Degree of intolerance to predicted Loss-of-Function (pLoF) variation
|
| gene_score |
gene_properties/gene_scores/RVIS
|
0 |
7 |
456.15 KB |
Residual Variation Intolerance Score
|
| gene_score |
gene_properties/gene_scores/SFARI_gene_score
|
0 |
7 |
150.27 KB |
SFARI gene score release 01-13-2021
|
| gene_score |
gene_properties/gene_scores/SFARI_gene_score_2024_Q1
|
0 |
9 |
191.15 KB |
SFARI gene score 2024 Q1 release
|
| gene_score |
gene_properties/gene_scores/Satterstrom_Buxbaum_Cell_2020
|
0 |
6 |
617.19 KB |
TADA derived gene-autism association score
|
| gene_score |
gene_properties/gene_scores/pLI
|
0 |
7 |
893.35 KB |
Probability of Loss-of-Function Intolerance
|
| gene_score |
gene_properties/gene_scores/pRec
|
0 |
7 |
895.18 KB |
Probability of biallelic loss-of-function intolerance |
| gene_set |
gene_properties/gene_sets/GO
|
0 |
4 |
12.07 MB |
GO (Gene Ontology) gene sets
|
| gene_set |
gene_properties/gene_sets/GO_2024-06-17_release
|
0 |
9 |
50.78 MB |
GO terms 2024-06-17 release
|
| gene_set |
gene_properties/gene_sets/MSigDB_curated
|
0 |
3 |
3.12 MB |
MSigDB (Molecular Signatures Database) gene sets derived from a variety of curated sources |
| gene_set |
gene_properties/gene_sets/PFAM_37.0_domains
|
0 |
7 |
2.84 MB |
PFAM 37.0 domains
|
| gene_set |
gene_properties/gene_sets/autism
|
0 |
7 |
4.43 KB |
Autism gene sets derived from publications |
| gene_set |
gene_properties/gene_sets/disease
|
0 |
3 |
66.81 KB |
Gene-disease associations
|
| gene_set |
gene_properties/gene_sets/domain
|
0 |
3 |
391.24 KB |
Protein domains or motifs
|
| gene_set |
gene_properties/gene_sets/main
|
0 |
17 |
103.97 KB |
Variety of gene sets with potential relevance to autism |
| gene_set |
gene_properties/gene_sets/miRNA
|
0 |
4 |
1.6 MB |
miRNA target sets |
| gene_set |
gene_properties/gene_sets/miRNA_Darnell
|
0 |
3 |
95.2 KB |
miRNA target sets by Darnell |
| gene_set |
gene_properties/gene_sets/relevant
|
0 |
15 |
101.82 KB |
Variety of gene sets with potential relevance to autism
|
| gene_set |
gene_properties/gene_sets/sfari
|
0 |
11 |
11.6 KB |
SFARI gene sets with relevance to autism
|
| gene_set |
gene_properties/gene_sets/spark
|
0 |
5 |
1.29 KB |
SPARK gene sets with relevance to autism
|
| gene_score |
hg19/enrichment/coding_length_in_target_ref_gene_v20190211
|
0 |
5 |
111.22 KB |
Coding length in target enrichment background using refGene gene models for HG19 from 20190211
|
| gene_score |
hg19/enrichment/coding_length_ref_gene_v20190211
|
0 |
5 |
162.32 KB |
Coding length enrichment background using refGene gene models for HG19 from 20190211
|
| gene_models |
hg19/gene_models/ccds_v201309
|
0 |
5 |
2.56 MB |
CCDS (Consensus CDS) gene model 2013 |
| gene_models |
hg19/gene_models/knownGene_v201304
|
0 |
5 |
5.5 MB |
knownGene gene model 2013 |
| gene_models |
hg19/gene_models/refGeneMito_v201309
|
0 |
5 |
3.98 MB |
RefGene gene model 2013 with mitochondrial genes
|
| gene_models |
hg19/gene_models/refGene_v201309
|
0 |
5 |
3.98 MB |
RefGene gene model 2013
|
| gene_models |
hg19/gene_models/refGene_v20190211
|
0 |
5 |
5.47 MB |
RefGene gene model 2019
|
| genome |
hg19/genomes/GATK_ResourceBundle_5777_b37_phiX174
|
0 |
92 |
2.94 GB |
HG19 reference genome
|
| position_score |
hg19/phastCons46_placentals
|
0 |
9 |
20.19 GB |
Conservation score based on the multiple alignment of 46 species using placental species
|
| position_score |
hg19/phastCons46_primates
|
0 |
6 |
20.18 GB |
Conservation score based on the multiple alignment of 46 species using primate species
|
| position_score |
hg19/phastCons46_vertebrates
|
0 |
6 |
20.18 GB |
Conservation score based on the multiple alignment of 46 species using vertebrate species
|
| position_score |
hg19/phyloP46_placentals
|
0 |
6 |
8.02 GB |
Conservation score based on the multiple alignment of 46 species using placental species
|
| position_score |
hg19/phyloP46_primates
|
0 |
6 |
20.18 GB |
Conservation score based on the multiple alignment of 46 species using primate species
|
| position_score |
hg19/phyloP46_vertebrates
|
0 |
6 |
20.18 GB |
Conservation score based on the multiple alignment of 46 species using vertebrate species
|
| np_score |
hg19/scores/CADD
|
0 |
10 |
79.37 GB |
CADD score for functional prediction of a SNP
|
| position_score |
hg19/scores/FitCons-i6-merged
|
0 |
8 |
105.18 MB |
fitCons (fitness consequences) score estimates selective pressure on genomic positions.
|
| position_score |
hg19/scores/FitCons2_E035
|
0 |
8 |
291.52 MB |
FitCons2 score computed for the Primary haematopoietic stem cells (HSCs) (E035).
|
| position_score |
hg19/scores/FitCons2_E067
|
0 |
8 |
260.98 MB |
Cell-type specific FitCons scores for Brain Angular Gyrus tissue (E067).
|
| position_score |
hg19/scores/FitCons2_E068
|
0 |
8 |
270.23 MB |
Cell-type specific FitCons scores for Brain Anterior Caudate tissue (E068).
|
| position_score |
hg19/scores/FitCons2_E069
|
0 |
8 |
262.14 MB |
Cell-type specific FitCons scores for Brain Cingulate Gyrus tissue (E069).
|
| position_score |
hg19/scores/FitCons2_E070
|
0 |
8 |
262.33 MB |
Cell-type specific FitCons scores for Brain Germinal Matrix tissue (E070).
|
| position_score |
hg19/scores/FitCons2_E071
|
0 |
8 |
255.46 MB |
Cell-type specific FitCons scores for Brain Hippocampus Middle tissue (E071).
|
| position_score |
hg19/scores/FitCons2_E072
|
0 |
8 |
257.62 MB |
Cell-type specific FitCons scores for Brain Inferior Temporal Lobe tissue (E072).
|
| position_score |
hg19/scores/FitCons2_E073
|
0 |
8 |
266.96 MB |
FitCons2 score computed for the Brain Dorsolateral Prefrontal Cortex (E073) tissue.
|
| position_score |
hg19/scores/FitCons2_E074
|
0 |
8 |
262.13 MB |
Cell-type specific FitCons scores for Brain Substantia Nigra tissue (E074).
|
| position_score |
hg19/scores/FitCons2_E081
|
0 |
8 |
276.04 MB |
Cell-type specific FitCons scores for Fetal Brain Male tissue (E081).
|
| position_score |
hg19/scores/FitCons2_E082
|
0 |
8 |
278.89 MB |
Cell-type specific FitCons scores for Fetal Brain Female tissue (E082).
|
| position_score |
hg19/scores/Linsight
|
0 |
8 |
1.35 GB |
LINSIGHT score quantifies the likelihood of negative selection on noncoding sites.
|
| np_score |
hg19/scores/MPC
|
0 |
9 |
2.26 GB |
MPC (Missense badness, PolyPhen-2, and Constraint) is a composite score that predicts the impact of missense variants.
|
| position_score |
hg19/scores/phastCons46_placentals
|
0 |
8 |
10.55 GB |
phastCons46_placentals is a conservation score based on the
placental mammal subset of species
|
| position_score |
hg19/scores/phastCons46_primates
|
0 |
8 |
14.02 GB |
phastCons46_primates is a conservation score based on the
primates subset of species
|
| position_score |
hg19/scores/phastCons46_vertebrates
|
0 |
8 |
10.81 GB |
phastCons46_vertebrates is a conservation score based on a multiple alignments
of 45 vertebrate genomes to the human genome.
|
| position_score |
hg19/scores/phyloP46_placentals
|
0 |
8 |
14.62 GB |
phyloP (phylogenetic p-values) conservation score based on the multiple
alignments of the placental mammal species
|
| position_score |
hg19/scores/phyloP46_primates
|
0 |
8 |
10.81 GB |
phyloP (phylogenetic p-values) conservation score based on the multiple
alignments of the primate species
|
| position_score |
hg19/scores/phyloP46_vertebrates
|
0 |
8 |
14.72 GB |
phyloP (phylogenetic p-values) conservation score based on the multiple
alignments of 46 vertebrate genomes
|
| allele_score |
hg19/variant_frequencies/gnomAD_v2.1.1/exomes
|
0 |
32 |
959.44 MB |
gnomAD exomes v2.1.1 variants build from ~260,000 whole exome samples
published by the Broad Institute.
|
| allele_score |
hg19/variant_frequencies/gnomAD_v2.1.1/genomes
|
0 |
31 |
12.27 GB |
gnomAD genomes v2.1.1 variants build from ~32,000 whole genome sequencing samples
published by the Broad Institute.
|
| gene_score |
hg38/enrichment/coding_length_ref_gene_v20170601
|
0 |
5 |
159.31 KB |
Coding length enrichment background
using refGene gene models for HG38 from 20170601
|
| gene_score |
hg38/enrichment/ur_synonymous_AGRE_WG38_859
|
0 |
5 |
174.87 KB |
Ultra rare synonymous enrichment background build from AGRE WGS CSHL.
|
| gene_score |
hg38/enrichment/ur_synonymous_SFARI_SSC_WGS_2
|
0 |
5 |
186.79 KB |
Ultra rare synonymous enrichment background build from SFARI SSC WGS NYGC.
|
| gene_score |
hg38/enrichment/ur_synonymous_SFARI_SSC_WGS_CSHL
|
0 |
5 |
186.25 KB |
Ultra rare synonymous enrichment background build from SFARI SSC WGS NYGC.
|
| gene_score |
hg38/enrichment/ur_synonymous_iWES_v1_1
|
0 |
5 |
192.94 KB |
Ultra rare synonymous enrichment background build from SPARK iWES v1.1.
|
| gene_score |
hg38/enrichment/ur_synonymous_iWES_v2
|
0 |
5 |
196.06 KB |
Ultra rare synonymous enrichment background build from SPARK iWES v2.
|
| gene_score |
hg38/enrichment/ur_synonymous_iWGS_v1_1
|
0 |
5 |
193.11 KB |
Ultra rare synonymous enrichment background build from SPARK iWGS v1.1.
|
| gene_score |
hg38/enrichment/ur_synonymous_w1202s766e611_liftover
|
0 |
5 |
178.49 KB |
Ultra rare synonymous enrichment background build from SFARI SSC WES CSHL liftover.
|
| gene_models |
hg38/gene_models/GENCODE/34/basic/ALL
|
0 |
8 |
36.64 MB |
GENCODE 34, basic gene annotation on the reference chromosomes, scaffolds, assembly patches and alternate loci (haplotypes)
|
| gene_models |
hg38/gene_models/GENCODE/34/basic/CHR
|
0 |
8 |
33.62 MB |
GENCODE 34, basic gene annotation on the reference chromosomes only
|
| gene_models |
hg38/gene_models/GENCODE/34/comprehensive/ALL
|
0 |
8 |
60.26 MB |
GENCODE 34, comprehensive gene annotation on the reference chromosomes, scaffolds, assembly patches and alternate loci (haplotypes)
|
| gene_models |
hg38/gene_models/GENCODE/34/comprehensive/CHR
|
0 |
8 |
55.62 MB |
GENCODE 34, comprehensive gene annotation on the reference chromosomes only
|
| gene_models |
hg38/gene_models/GENCODE/34/comprehensive/PRI
|
0 |
8 |
55.63 MB |
GENCODE 34, comprehensive gene annotation on the primary assembly (chromosomes and scaffolds) sequence regions
|
| gene_models |
hg38/gene_models/GENCODE/46/basic/ALL
|
0 |
8 |
41.47 MB |
GENCODE 46, basic gene annotation on the reference chromosomes, scaffolds, assembly patches and alternate loci (haplotypes)
|
| gene_models |
hg38/gene_models/GENCODE/46/basic/CHR
|
0 |
8 |
38.04 MB |
GENCODE 46, basic gene annotation on the reference chromosomes only
|
| gene_models |
hg38/gene_models/GENCODE/46/basic/PRI
|
0 |
8 |
38.05 MB |
GENCODE 46, basic gene annotation on the primary assembly (chromosomes and scaffolds) sequence regions
|
| gene_models |
hg38/gene_models/GENCODE/46/comprehensive/ALL
|
0 |
8 |
69.71 MB |
GENCODE 46, comprehensive gene annotation on the reference chromosomes, scaffolds, assembly patches and alternate loci (haplotypes)
|
| gene_models |
hg38/gene_models/GENCODE/46/comprehensive/CHR
|
0 |
8 |
64.42 MB |
GENCODE 46, comprehensive gene annotation on the reference chromosomes only
|
| gene_models |
hg38/gene_models/GENCODE/46/comprehensive/PRI
|
0 |
8 |
64.44 MB |
GENCODE 46, comprehensive gene annotation on the primary assembly (chromosomes and scaffolds) sequence regions
|
| gene_models |
hg38/gene_models/MANE/0.5
|
0 |
8 |
5.51 MB |
MANE gene model version 0.5
|
| gene_models |
hg38/gene_models/MANE/0.6
|
0 |
8 |
6.09 MB |
MANE gene model version 0.6
|
| gene_models |
hg38/gene_models/MANE/0.7
|
0 |
8 |
6.43 MB |
MANE gene model version 0.7
|
| gene_models |
hg38/gene_models/MANE/0.8
|
0 |
8 |
6.94 MB |
MANE gene model version 0.8
|
| gene_models |
hg38/gene_models/MANE/0.9
|
0 |
8 |
7.48 MB |
MANE gene model version 0.9
|
| gene_models |
hg38/gene_models/MANE/0.91
|
0 |
8 |
8.39 MB |
MANE gene model version 0.91
|
| gene_models |
hg38/gene_models/MANE/0.92
|
0 |
8 |
8.71 MB |
MANE gene model version 0.92
|
| gene_models |
hg38/gene_models/MANE/0.93
|
0 |
8 |
9.18 MB |
MANE gene model version 0.93
|
| gene_models |
hg38/gene_models/MANE/0.95
|
0 |
8 |
9.65 MB |
MANE gene model version 0.95
|
| gene_models |
hg38/gene_models/MANE/1.0
|
0 |
8 |
9.92 MB |
MANE gene model version 1.0
|
| gene_models |
hg38/gene_models/MANE/1.1
|
0 |
8 |
10.82 MB |
MANE gene model version 1.1
|
| gene_models |
hg38/gene_models/MANE/1.2
|
0 |
8 |
10.86 MB |
MANE gene model version 1.2
|
| gene_models |
hg38/gene_models/MANE/1.3
|
0 |
8 |
10.88 MB |
MANE gene model version 1.3
|
| gene_models |
hg38/gene_models/refGene_v20170601
|
0 |
5 |
5.45 MB |
refSeq gene models for HG38 from 20170601
|
| gene_models |
hg38/gene_models/refSeq_v20200330
|
0 |
5 |
4.19 MB |
refSeq gene models for HG38 from 2020-03
Default gene models used by GPF for HG38.
|
| gene_models |
hg38/gene_models/refSeq_v20240129
|
0 |
5 |
7.03 MB |
refSeq gene models for HG38 from 2024-01-29
|
| genome |
hg38/genomes/GRCh38-hg38
|
0 |
3374 |
3.04 GB |
HG38 reference genome
|
| genome |
hg38/genomes/GRCh38.p13
|
0 |
646 |
3.09 GB |
Nucleotide sequence of the GRCh38.p13 genome assembly
|
| genome |
hg38/genomes/GRCh38.p14
|
0 |
715 |
3.95 GB |
Nucleotide sequence of the GRCh38.p14 genome assembly
|
| np_score |
hg38/scores/CADD_v1.4
|
0 |
18 |
79.42 GB |
CADD (Combined Annotation Dependent Depletion score) predicts the potential impact of a SNP
|
| np_score |
hg38/scores/CADD_v1.6
|
0 |
12 |
80.65 GB |
CADD (Combined Annotation Dependent Depletion score) predicts the potential impact of a SNP
|
| allele_score |
hg38/scores/clinvar_20221105
|
0 |
44 |
115.29 MB |
Measure used to assess the clinical significance of genetic variants
|
| position_score |
hg38/scores/phastCons100way
|
0 |
6 |
5.48 GB |
Conservation score based on the multiple alignment of 100 species
|
| position_score |
hg38/scores/phastCons20way
|
0 |
6 |
6.63 GB |
Conservation score based on the multiple alignment of 20 species
|
| position_score |
hg38/scores/phastCons30way
|
0 |
6 |
6.59 GB |
Conservation score based on the multiple alignment of 30 species
|
| position_score |
hg38/scores/phastCons7way
|
0 |
6 |
7.19 GB |
Conservation score based on the multiple alignment of 7 species
|
| position_score |
hg38/scores/phyloP100way
|
0 |
6 |
9.19 GB |
Conservation score based on the multiple alignment of 100 species
|
| position_score |
hg38/scores/phyloP20way
|
0 |
6 |
7.33 GB |
Conservation score based on the multiple alignment of 20 species
|
| position_score |
hg38/scores/phyloP30way
|
0 |
6 |
7.82 GB |
Conservation score based on the multiple alignment of 30 species
|
| position_score |
hg38/scores/phyloP7way
|
0 |
6 |
5.25 GB |
Conservation score based on the multiple alignment of 7 species
|
| allele_score |
hg38/variant_frequencies/SSC_WG38_CSHL_2380
|
0 |
12 |
783.71 MB |
Exported from SFARI_SSC_WGS_CSHL using `gpf_validation_data/data_hg38/exports/SFARI_SSC_WGS_CSHL_frequency`.
|
| allele_score |
hg38/variant_frequencies/gnomAD_4.1.0/exomes/ALL
|
0 |
21 |
1.32 GB |
gnomAD v4.1.0 exome variants (ALL)
|
| allele_score |
hg38/variant_frequencies/gnomAD_4.1.0/exomes/afr
|
0 |
21 |
172.93 MB |
gnomAD v4.1.0 exome variants (African/African American)
|
| allele_score |
hg38/variant_frequencies/gnomAD_4.1.0/exomes/amr
|
0 |
21 |
171.3 MB |
gnomAD v4.1.0 exome variants (Ad Mixed American)
|
| allele_score |
hg38/variant_frequencies/gnomAD_4.1.0/exomes/asj
|
0 |
21 |
56.02 MB |
gnomAD v4.1.0 exome variants (Ashkenazi Jewish)
|
| allele_score |
hg38/variant_frequencies/gnomAD_4.1.0/exomes/eas
|
0 |
21 |
149.24 MB |
gnomAD v4.1.0 exome variants (East Asian)
|
| allele_score |
hg38/variant_frequencies/gnomAD_4.1.0/exomes/fin
|
0 |
21 |
90.37 MB |
gnomAD v4.1.0 exome variants (Finnish)
|
| allele_score |
hg38/variant_frequencies/gnomAD_4.1.0/exomes/mid
|
0 |
21 |
62.78 MB |
gnomAD v4.1.0 exome variants (Middle Eastern)
|
| allele_score |
hg38/variant_frequencies/gnomAD_4.1.0/exomes/nfe
|
0 |
21 |
916.58 MB |
gnomAD v4.1.0 exome variants (Non-Finnish European)
|
| allele_score |
hg38/variant_frequencies/gnomAD_4.1.0/exomes/sas
|
0 |
21 |
277.15 MB |
gnomAD v4.1.0 exome variants (South Asian)
|
| allele_score |
hg38/variant_frequencies/gnomAD_4.1.0/genomes/ALL
|
0 |
21 |
10.47 GB |
gnomAD v4.1.0 genome variants (ALL)
|
| allele_score |
hg38/variant_frequencies/gnomAD_4.1.0/genomes/afr
|
0 |
21 |
5.98 GB |
gnomAD v4.1.0 genome variants (African/African American)
|
| allele_score |
hg38/variant_frequencies/gnomAD_4.1.0/genomes/amr
|
0 |
21 |
4.0 GB |
gnomAD v4.1.0 genome variants (Ad Mixed American)
|
| allele_score |
hg38/variant_frequencies/gnomAD_4.1.0/genomes/asj
|
0 |
21 |
2.27 GB |
gnomAD v4.1.0 genome variants (Ashkenazi Jewish)
|
| allele_score |
hg38/variant_frequencies/gnomAD_4.1.0/genomes/eas
|
0 |
21 |
3.03 GB |
gnomAD v4.1.0 genome variants (East Asian)
|
| allele_score |
hg38/variant_frequencies/gnomAD_4.1.0/genomes/fin
|
0 |
21 |
2.86 GB |
gnomAD v4.1.0 genome variants (Finnish)
|
| allele_score |
hg38/variant_frequencies/gnomAD_4.1.0/genomes/mid
|
0 |
21 |
1.93 GB |
gnomAD v4.1.0 genome variants (Middle Eastern)
|
| allele_score |
hg38/variant_frequencies/gnomAD_4.1.0/genomes/nfe
|
0 |
21 |
5.75 GB |
gnomAD v4.1.0 genome variants (Non-Finnish European)
|
| allele_score |
hg38/variant_frequencies/gnomAD_4.1.0/genomes/sas
|
0 |
21 |
3.04 GB |
gnomAD v4.1.0 genome variants (South Asian)
|
| allele_score |
hg38/variant_frequencies/gnomAD_v2.1.1_liftover/exomes
|
0 |
35 |
928.26 MB |
Liftover of gnomAD exomes v2.1.1 to hg38.
|
| allele_score |
hg38/variant_frequencies/gnomAD_v2.1.1_liftover/genomes
|
0 |
35 |
11.53 GB |
Liftover of gnomAD genomes v2.1.1 to hg38.
|
| allele_score |
hg38/variant_frequencies/gnomAD_v3/genomes
|
0 |
18 |
17.64 GB |
gnomAD v3.0 variants built from ~150,000 samples with whole genome sequence data.
|
| liftover_chain |
liftover/hg19ToHg38
|
0 |
6 |
450.24 KB |
Liftover Chain Hg19 to Hg38
|
| liftover_chain |
liftover/hg38ToHg19
|
0 |
6 |
2.4 MB |
Liftover Chain Hg38 to Hg19
|