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
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