How to FLAG low quality SNPs in samtools VCF

Question

[hellbio]

Dear all,

I have been using the below command to remove low quality SNPs from VCF generated through samtools mpileup and bcftools.

vcfutils.pl varFilter -Q 40 -d 10 input.vcf | awk '$6>=40' > output.vcf

However, how can i only flag these variants as LOWQual within the VCF instead of removing from the VCF generated by mpileup/bcftools.

I know GATK has something to FLAG variants. In this case the VCF is from mpileup/bcftools which may not have the required annotation to work with GATK. Could someone point a way to do this.

Answer 1

[finswimmer]

Hello,

use bcftools filter to set a Flag in in the FILTER column;

$ bcftools filter -e 'QUAL<40' -s "LowQual" input.vcf

fin swimmer