Question

QUAL in VCF file

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2.1 years ago

Maryam ▴ 10

Hello, I am learning the sequencing data and working with VCF files now. I want to know what does Qual '.' means. Does this mean that quality of my variant has not been calculated?

Thank you

NGS Variant VCF • 1.1k views

ADD COMMENT • link updated 13 months ago by Ram 43k • written 2.1 years ago by Maryam ▴ 10

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Does this mean that quality of my variant has not been calculated?

yes , not-available, not-calculated, unknown

ADD REPLY • link 2.1 years ago by Pierre Lindenbaum 161k

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Thank you so much

ADD REPLY • link 2.1 years ago by Maryam ▴ 10

score 2 · Accepted Answer · 2022-03-15

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.