I am trying to filter based on GQ < 15. I do the following:
vcftools --vcf infile.vcf --minGQ 15 --recode --out filtered
However, this filtering does not work, nothing is being removed:
After filtering, kept 1287174 out of a possible 1287174 Site
I confirm that the GQ tag is present in my VCF file. Other filters such as min/maxDP or minQ work just fine. I am using VCFtools - v0.1.13
Any thoughts on this would be greatly appreciated.
p.s: This is a cross-post from SEQanswer where I did not receive any answers: http://seqanswers.com/forums/showthread.php?t=69468