Originally, I thought each line of a VCF file represented a single read that resulted in the detection of a variant. In that case, the QUAL field was straight forward, it was the quality of that read. However, when you have multiple samples, it seems the line is now just used to store the variants that were discovered at that location across a number of samples. So that would be the result of multiple read in multiple sequencing runs per sample. So the QUAL field is now making no sense to me.
I think I have a fundamental misunderstanding of what I single record in a VCF file is and this QUAL question is evidence in that direction of total misunderstanding. Any help is appreciated.
1 answer
Even if you have a single sample, each line correspond to a genomic position (site), not a single read. The definition of the QUAL field should be specified in the header. For instance, the iterative gVCF genotyper defines the QUAL field as: the maximum of the input QUAL values for the site across the global cohort.
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