How to FLAG low quality SNPs in samtools VCF
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Entering edit mode
4.5 years ago
hellbio ▴ 520

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.

samtools VCF • 1.1k views
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1
Entering edit mode
4.5 years ago

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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