VCF: run `solve_blocks()` on typed SNPs only

biona001 / GhostKnockoffGWAS

Knockoff-based analysis of GWAS summary statistics data

MIT License

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VCF: run `solve_blocks()` on typed SNPs only #12

Open biona001 opened 4 months ago

biona001 commented 4 months ago

Some VCF files might have imputed SNPs.

In ~/knockoffs/400phenotypes-part1.ipynb on Sherlock, I have some code to compute group representatives only on the typed variants. Putting this here in case I forget.