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!
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!
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