not getting values for Filter columns with vcf files generated using SAMTOOLS Mpileup
How to set values for Filter columns with SAMTOOLS vcf files. I am getting "." for all VCF entries.
Is it normal or i need to set some parameters with command ?
This is command : samtools mpileup -DguS -f PMC01-01.bam | bcftools call -vmO z -o PMC01-01.vcf.gz
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No filters have been applied, so only
.should appear. See the VCF spec.Yes , How I can applied filter while running variant calling with SAMTools ? I
bcftools filter [OPTIONS] FILE (see:https://samtools.github.io/bcftools/bcftools.html )