When both these options are used in the rvtest command --peopleExcludeID and --freqUpper ,
Does rvtest first exclude the samples listed, and then calculate the new allele frequency at sites, and then check against the provided threshold (XF) ? Or
Does rvtest first calculate the site's allele frequency, then check against provided threshold (XF), and then perform the sample exclusion ?
Can you also put this explanation up on the Wiki page for other users, similar to plink https://www.cog-genomics.org/plink/1.9/order
My question would also hold for other Variant Site filter options along with other Sample filter options.
When both these options are used in the rvtest command --peopleExcludeID and --freqUpper , Does rvtest first exclude the samples listed, and then calculate the new allele frequency at sites, and then check against the provided threshold (XF) ? Or
Does rvtest first calculate the site's allele frequency, then check against provided threshold (XF), and then perform the sample exclusion ?
Can you also put this explanation up on the Wiki page for other users, similar to plink https://www.cog-genomics.org/plink/1.9/order My question would also hold for other Variant Site filter options along with other Sample filter options.
Thank You, Samreen