Thouis R Jones

Thanks for the idea, but there appear to be thousands of files in those directories which will take days to extract the variants.  Is there a pre-existing list of passing variants, or a faster way ...

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• 13 February 2026 21:45
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Thanks.  Unfortunately, PLINK2 filters donors first and then variants, so that requires creating a new set of variant files before running a GWAS.  (https://www.cog-genomics.org/plink/2.0/order)I'm...

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• 02 February 2026 14:43
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Looking deeper at the per-variant missingness rates, this appears to be partly from the large relative size of the centromeric region (7% of the chromosome length) and the number of variants in tha...

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• 08 January 2026 19:11
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