I am learning GWAS study and PRS for predicting disease. I was aligning my sequencing data with GRCH38 reference panel. However, in the PRS analysis step, I found that most of the summary statistics are developed in GRCH37. It was a bit inconvenient for me because I have to convert vcf/snp file into GRCH37 which may end up losing some snps. I was checking this database link. Is there any database of summary statistics in GRCH38?
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$\begingroup$ It's a good question, could you please consider upvoting/accepting the answer by user438383. It's definitely useful IMO. $\endgroup$– M__ ♦Sep 15 at 16:11
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2 Answers
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This is a common issue. Instead of lifting over your genomes, it might be computationally and conceptually easier just to lift over the summary statistics to GRCh37. Alternatively (and preferably), this is done for you for every GWAS published in the GWAS catalog. Simply click on the "harmonized" folder after clicking on "download" and you can download whatever build aligns with your genotype data.
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$\begingroup$ I am sticking with generating vcf in GRCH37. Thanks anyway. $\endgroup$ Oct 29 at 18:19
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$\begingroup$ @ShafayetRahat You'll also need to ensure the scorefile is b37 too $\endgroup$ Oct 29 at 19:07
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