Help finding GTEx v8 Imputed Genotypes

Question

[JourneyToAbyss]

I have access to the GTEx project and have downloaded v8 genotypes from gen3 AnVIL (It appears v7 is on dbGaP and other files are available through Anvil Terra).

I read that GTEx has made the imputed genotypes available (e.g. what IMPUTE2 or Michigan server does). However, I can not find any file manifest concerning the protected data on the GTEx website or the gen3 Anvil platform. There are files labeled with SHAPEIT, a software used for phasing, which is needed prior to imputation. But I am unsure if these files have been imputed (On the Michigan Server or elsewhere).

If anyone could point me in the right direction, that would be appreciated.

Here are some file names: GTEx_Analysis_2017-06-05_v8_WholeGenomeSeq_866Indiv.vcf.gz (253.03 GB) GTEx_Analysis_2017-06-05_v8_WholeGenomeSeq_838Indiv_Analysis_Freeze.vcf.gz (174.1 GB) phASER_GTEx_v8_merged.vcf.gz (9.73 GB) phASER_WASP_GTEx_v8_merged.vcf.gz (9.62 GB) GTEx_Analysis_2017-06-05_v8_WholeGenomeSeq_866Indiv_sites_VEP_annot.vcf.gz (8.89 GB) GTEx_Analysis_2017-06-05_v8_WholeGenomeSeq_838Indiv_Analysis_Freeze.SHAPEIT2_phased.vcf.gz (3.73 GB) GTEx_Analysis_2017-06-05_v8_WholeExomeSeq_979Indiv_VEP_annot.vcf.gz (3.65 GB) GTEx_Analysis_2017-06-05_v8_WholeGenomeSeq_838Indiv_Analysis_Freeze.SHAPEIT2_phased.MAF01.bed (2.11 GB) GTEx_Analysis_2017-06-05_v8_WholeGenomeSeq_838Indiv_Analysis_Freeze.SHAPEIT2_phased.MAF01.vcf.gz (2.1 GB)

Thank you!

[7ehuang]

were you ever able to locate phASER_GTEx_v8_merged.vcf.gz and phASER_WASP_GTEx_v8_merged.vcf.gz? i'm also having trouble finding that file (even with access to dbGAP phs000424). i was able to download the SHAPEIT2 VCF files from dbGAP though.

Answer 1

[vdauwera]

Hi, have you asked the AnVIL or Terra support teams for help with this? They should be able to help you track down the information you're looking for — at least whether that data is available through AnVIL or not.