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choishingwan / PRSice

A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores
http://prsice.info
GNU General Public License v3.0
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[BUG] maf filter #308

Open JihyunKiminGithub opened 2 years ago

JihyunKiminGithub commented 2 years ago

Dear developers,

Thank you for making this wonderful tool. I want to know how --maf works at this PRSice software. Before running the prsice software, I calculated MAF of snps by using --freq function of plink2. While running PRSice, I set the maf function as (--maf 0.01) with small dataset and I found 3 snps were excluded due to maf criteria.

When I looked at those maf, these were 0.0104089, 0.0102555, 0.0110307 which is larger than 0.01 which is contradictory with my expectation. Can you please explain why MAF filter criteria worked like this?

Thanks

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chrchang commented 2 years ago

plink2 normally excludes "nonfounders" (i.e. any sample with parental IDs listed in the .fam/.psam file) from its MAF calculation. This results in small MAF differences from other programs which don't do the same thing.