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broadinstitute / gtex-v8

Notebooks and scripts for reproducing analyses and figures from the V8 GTEx Consortium paper
BSD 3-Clause "New" or "Revised" License
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INDEL, Structural Variation in eQTL, sQTL #6

Closed Shicheng-Guo closed 2 years ago

Shicheng-Guo commented 2 years ago

Dear Team,

I am wondering whether INDEL, CNV and Structural Variation are included in eQTL and sQTL analysis? or only SNPs are included?

Thanks.

Shicheng

francois-a commented 2 years ago

Hi, SNPs and indels were included in the core QTL analyses (you can see this in the summary statistics files, since the variants are encoded as chr_pos_ref_alt_build). QTLs for SV and STRs were reported in separate studies, in https://www.nature.com/articles/ng.3834 and https://www.nature.com/articles/s41588-019-0521-9.

Shicheng-Guo commented 2 years ago

Great. Thanks. eSTRs and eSV can also be donwloaded from GTEx website, correct? Shicheng

francois-a commented 2 years ago

The SV data is available from the GTEx Portal, under "GTEx Analysis V6". The STR data is available at http://webstr.ucsd.edu/ (STR calls are on AnVIL/dbGaP).