Comments (4)
chrchang
commented on September 25, 2024
The lower-MAF SNP is pruned. If the MAFs are equal, the later-position SNP is pruned.
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KehaoWu
commented on September 25, 2024
Is it possible that incorporate p values or function information into SNP prunning?
For example, the smaller p-value SNP is pruned. If the p-values are equal, the intergenic SNP is pruned.
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chrchang
commented on September 25, 2024
You can currently get this behavior by creating an artificial set of "MAF estimates" which are a function of p-value and gene positions, and loading that with --read-freq. (Just make sure to not include any filters which actually depend on MAF in your run...)
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KehaoWu
commented on September 25, 2024
Good idea! Thank you!
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