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From: Antoine P. <ant...@gm...> - 2016-05-31 14:07:52
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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 |