[Vcftools-help] vcftools --minGQ not filtering

[Antoine P. <ant...@gm...>]

Hello,

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.

Thanks,
Antoine