Help finding GTEx v8 Imputed Genotypes
Entering edit mode
28 days ago

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!

SHAPEIT GTEx • 210 views
Entering edit mode
6 days ago
vdauwera ★ 1.2k

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.


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