Type ID Version Number of files Size in bytes (total) Summary
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 7 532.4 KB Gene vulnerability/intolerance score based on the rare LGD variants
gene_score gene_properties/gene_scores/LOEUF 0 23 13.28 MB Degree of intolerance to predicted Loss-of-Function (pLoF) variation
gene_score gene_properties/gene_scores/RVIS 0 7 450.6 KB Residual Variation Intolerance Score
gene_score gene_properties/gene_scores/SFARI_gene_score 0 7 143.81 KB SFARI gene score release 01-13-2021
gene_score gene_properties/gene_scores/SFARI_gene_score_2024_Q1 0 9 184.54 KB SFARI gene score 2024 Q1 release
gene_score gene_properties/gene_scores/Satterstrom_Buxbaum_Cell_2020 0 6 613.42 KB TADA derived gene-autism association score
gene_score gene_properties/gene_scores/pLI 0 7 893.11 KB Probability of Loss-of-Function Intolerance
gene_score gene_properties/gene_scores/pRec 0 7 894.94 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/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/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 5 106.71 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 5 157.76 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
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 8 105.17 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 8 260.97 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 8 262.13 MB Cell-type specific FitCons scores for Brain Cingulate Gyrus tissue (E069).
position_score hg19/scores/FitCons2_E070 0 8 262.32 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 8 257.61 MB Cell-type specific FitCons scores for Brain Inferior Temporal Lobe tissue (E072).
position_score hg19/scores/FitCons2_E073 0 8 266.95 MB FitCons2 score computed for the Brain Dorsolateral Prefrontal Cortex (E073) tissue.
position_score hg19/scores/FitCons2_E074 0 8 262.12 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 8 278.88 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 5 154.79 KB Coding length enrichment background using refGene gene models for HG38 from 20170601
gene_score hg38/enrichment/ur_synonymous_AGRE_WG38_859 0 5 168.8 KB Ultra rare synonymous enrichment background build from AGRE WGS CSHL.
gene_score hg38/enrichment/ur_synonymous_SFARI_SSC_WGS_2 0 5 180.76 KB Ultra rare synonymous enrichment background build from SFARI SSC WGS NYGC.
gene_score hg38/enrichment/ur_synonymous_SFARI_SSC_WGS_CSHL 0 5 180.24 KB Ultra rare synonymous enrichment background build from SFARI SSC WGS NYGC.
gene_score hg38/enrichment/ur_synonymous_iWES_v1_1 0 5 186.89 KB Ultra rare synonymous enrichment background build from SPARK iWES v1.1.
gene_score hg38/enrichment/ur_synonymous_iWES_v2 0 5 190.01 KB Ultra rare synonymous enrichment background build from SPARK iWES v2.
gene_score hg38/enrichment/ur_synonymous_iWGS_v1_1 0 5 187.1 KB Ultra rare synonymous enrichment background build from SPARK iWGS v1.1.
gene_score hg38/enrichment/ur_synonymous_w1202s766e611_liftover 0 5 172.46 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 44 115.55 MB Measure used to assess the clinical significance of genetic variants
position_score hg38/scores/phastCons100way 0 8 10.15 GB phastCons100way is a conservation score based on the multiple alignment of 100 species.
position_score hg38/scores/phastCons20way 0 8 13.6 GB phastCons20way is a conservation score based on the multiple alignment of 20 species.
position_score hg38/scores/phastCons30way 0 8 12.97 GB phastCons30way is a conservation score based on the multiple alignment of 30 species.
position_score hg38/scores/phastCons7way 0 11 14.64 GB phastCons7way is a conservation score based on the multiple alignment of 7 species.
position_score hg38/scores/phyloP100way 0 8 16.1 GB phyloP100way is a conservation score based on the multiple alignment of 100 species.
position_score hg38/scores/phyloP20way 0 8 14.56 GB phyloP20way is a conservation score based on the multiple alignment of 20 species.
position_score hg38/scores/phyloP30way 0 8 14.72 GB phyloP30way is a conservation score based on the multiple alignment of 30 species.
position_score hg38/scores/phyloP7way 0 8 12.54 GB phyloP7way is a 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_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