how to do the repeatability filtering of vcf files?

Question

[Max]

hi, I am trying to filer the snps(from 19 populations) for the population structure analysis. I've set some parameters like MAF, missing rate and depth. I saw some pappers filtered the snps with repeatability value but i don't understand what that is and use what tools to do that filering. Does anyone know? Thanks.

[Pierre Lindenbaum]

I saw some pappers filtered the snps with repeatability value

which papers ?

[Max]

Population Structure, Genetic Connectivity, and Signatures of Local Adaptation of the Giant Black Tiger Shrimp (Penaeus monodon) throughout the Indo-Pacific Region

[Pierre Lindenbaum]

let me fix that for you:

Nga T T Vu, Kyall R Zenger, Catarina N S Silva, Jarrod L Guppy, Dean R Jerry, Population Structure, Genetic Connectivity, and Signatures of Local Adaptation of the Giant Black Tiger Shrimp (Penaeus monodon) throughout the Indo-Pacific Region, Genome Biology and Evolution, Volume 13, Issue 10, October 2021, evab214, https://doi.org/10.1093/gbe/evab214