Test-drive the GATK tools and Best Practices pipelines on Terra
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QUAL score for monomorphic positions in VCF files
I used the EMIT_ALL_SITES option with Unified Genotyper.
For polymorphic sites, the quality score (QUAL field) corresponds to the Phred scaled probability that a REF/ALT polymorphism exists at this site given sequencing data.
But for monomorphic sites, (at this site, we have an homozygote for the reference allele), what is the definition of the quality score ? and how is it computed ?
Many thanks for your explanation.