How to understand SNPs excluded as invariant or singleton in population 2

[yuan102379]

Hi @hardingnj ,

This version of xpclr is good at calculating the xpclr value of big dataset.

However, there exists a question that I can not understand. Why does some SNPs were filtered by xplcr ? The related information come from the log information like this 👍
2020-08-05 00:29:49 : INFO : 63,443 SNPs excluded as invariant or singleton in population 2 2020-08-05 00:29:49 : INFO : 862,709/926,152 SNPs included in the analysis (93.15%)

Are there some standards to filter these SNPs ? or Why these SNPs were filtered ?

Could you provide a suggestion, please ?

Thanks a lot, hardingnj.

Yours,

Yuan

[hardingnj]

Hi @yuan102379 , please see the answer here: https://github.com/hardingnj/xpclr/issues/57#issuecomment-647453586 and https://github.com/hardingnj/xpclr/issues/59#issuecomment-664436938