Accelerate computeStats with plink2 --geno-counts - Githubissues

junyangq / snpnet

snpnet: Fast and scalable lasso/elastic-net solver for large SNP data

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Accelerate computeStats with plink2 --geno-counts #29

Closed yk-tanigawa closed 4 years ago

yk-tanigawa commented 4 years ago

PLINK2's --geno-counts can provide the number of individuals with

missing values MISSING_CT
non-missing values OBS_CT
REF/ALT HET_REF_ALT_CTS
ALT/ALT TWO_ALT_GENO_CTS and others summary statistics.

This computation is very fast.

I drafted a function compute_stats_from_gcount() to use the output from PLINK2 --geno-counts to speed up this genotype data pre-processing.

I am wondering if you could consider incorporating this function.

Thanks!