[Vcftools-help] Clarification on --thin option

[Card, D. C <dc...@ut...>]

Hello,

I’d just like to know how VCFtools goes about thinning sites. Does it simply find a SNP and ignore any others for the specified distance (i.e., always take the first SNP) or does it select random ones from a distance starting at SNP #1 (if others exist in the window)? One obviously leads to the same SNPs being present after filtering while the other will result in different sets of SNPs.

Thank you,
Daren


Daren Card
Ph.D. Candidate
Castoe Lab
University of Texas at Arlington
dc...@ut...<mailto:dc...@ut...>
www.darencard.net