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data_sources.md

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Raw

Raw data sources

An explanation of and sources of raw data.

1KG

(source) WGS for 1000 Genomes release 20181203. This release has SNVs only

GTEx

GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt (source)

A de-identified, open access version of the sample annotations available in dbGaP.

GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz (source)

GTEx combined TPM file

GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_reads.gct.gz (source)

GTEx combined gene read counts

GTEx_Analysis_v8_eQTL_covariates.tar.gz (source)

Covariates used during eQTL discovery. Make sure to decompress.

GTEx_Analysis_v8_eQTL.tar (source)

eGene and significant variant-gene associations based on permutations. Make sure to decompress.

gencode.v26.GRCh38.genes.gtf (source)

Gene-level model based on the GENCODE 26 transcript model, where isoforms were collapsed to a single transcript per gene.

GTEx_Analysis_2017-06-05_v8_Annotations_SubjectPhenotypesDS.txt Subject annotations available from dbGaP

GTEx_Analysis_2017-06-05_v8_WholeGenomeSeq_838Indiv_Analysis_Freeze.SHAPEIT2_phased.vcf.gz GTEx_Analysis_2017-06-05_v8_WholeGenomeSeq_838Indiv_Analysis_Freeze.SHAPEIT2_phased.vcf.gz.tbi WGS data for GTEx v8 individuals

Annotations

hg38.phyloP100way.bw (source) PhyloP 100way conservation scores from UCSC genome browser