SNP quality score and library prep methods

BlueBlue Posts: 24Member

I've had the same DNA sample sequenced using two different library prep methods, NEB-Next and Illumina-Nextera, the latter of which generates twice the number of reads than the former. When genotypes for the two samples are called individually using the UnifiedGenotyper, the read depth, DP for the Illumina-Nextera is roughly twice that of the NEB-Next but the quality score, QUAL, remains similar. I was expecting the QUAL to reflect the read depth but obviously this is not the case. Could you enlighten me?

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