Is 'QUAL' in vcf file the 'QVAL' in the paper?

IARCbioinfo / needlestack

Multi-sample somatic variant caller

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Is 'QUAL' in vcf file the 'QVAL' in the paper? #193

Closed isshamie closed 2 years ago

isshamie commented 2 years ago

Hello, I'm trying to understand what QUAL is- the max value I see is 1000. In the paper I see 'QVAL', and the max is 100.

Thanks!

mfoll commented 2 years ago

Hi, yes, the phred-scaled q-value (noted QVAL in the paper) is what we report in the VCF as "QUAL" (QUAL is the name imposed in the VCF specification).