QUAL in VCF file
1 answer
what does Qual '.' means.
Section 1.6 of the VCF specification (https://samtools.github.io/hts-specs/VCFv4.3.pdf) states:
In all cases, missing values are specified with a dot (‘.’)
Does this mean that quality of my variant has not been calculated?
Generally speaking, yes.
The exact details depends on the bioinformatics pipeline used to generate the VCF. It's theoretically possible that the variant caller assigned a QUAL, but a downstream step removed it. For example, a tool that merges a set of single-sample VCFs into a single multi-sample VCF might strip out the variant-level QUAL (and move it to a sample-specific FORMAT field) since the meaning of QUAL is different in those two VCFs.
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yes , not-available, not-calculated, unknown
Thank you so much