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getting GQ values with VCF using SAMTOOLS Mpileup

I am using SAMTools Version: 1.3 (using htslib 1.3) , How to get GQ score for my variants ? I have used this command. samtools mpileup -DguS -f PMC01-01.bam | bcftools call -vmO z -o PMC01-01.vcf.gz

samtools
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updated by Shane McCarthy Shane McCarthy • written by always_learning always_learning

1 answer

Add -f GQ to the bcftools call command.

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written by Shane McCarthy Shane McCarthy

How to set values for Filter columns with SAMTOOLS vcf files. I am getting "." for all VCF entries.

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written by always_learning always_learning

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