How to FLAG low quality SNPs in samtools VCF
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.
1 answer
Hello,
use bcftools filter to set a Flag in in the FILTER column;
$ bcftools filter -e 'QUAL<40' -s "LowQual" input.vcf
fin swimmer
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