How to set genotypes with low GQ to missing. in a vcf file.

Question

[Apprentice]

Hi.

I always appreciate all your help.

I have one vcf file (a.vcf).

"a.vcf"

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample131 sample138 sample908

chr12 104350956 . G T 147880 PASS AC=1;AF=0.250;AN=4 GT:AD:DP:GQ ./.:.:0 0/1:25,22:47:99 0/0:36,0:36:99 0/1:36,3:39:30

I would like to get "b.vcf" , which the genotypes with GQ<90 were set to missing, "./." as below.

"b.vcf2

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample131 sample138 sample908

chr12 104350956 . G T 147880 PASS AC=1;AF=0.250;AN=4 GT:AD:DP:GQ ./.:.:0 0/1:25,22:47:99 0/0:36,0:36:99 ./.:36,3:39:30

In the b.vcf, a genotype of sample908 was set to missing because of GQ<99 (GQ=30).

Could you tell me how to get the file?

I wuould like to get the file by using bcftools, if it's possible. If it's possible, could you tell me how to get the file using bcftools?

Answer 1

[silvia.shuchang.liu]

You can use vcftools '--minGQ' option for genotype quality filtering

vcftools --vcf a.vcf --minGQ 90 --out b --recode

A b.recode.vcf file will be generated.

Please check man vcftool for details, https://vcftools.github.io/man_latest.html