getting GQ values with VCF using SAMTOOLS Mpileup

Question

[always_learning]

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

Answer 1

[Shane McCarthy]

Add -f GQ to the bcftools call command.

[always_learning]

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