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Test-drive the GATK tools and Best Practices pipelines on Terra
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Calibration of QUAL field emitted by the Unified Genotyper
I am looking at the distribution of quality scores (QUAL column of VCF) emitted by the Unified Genotyper v1.4 (old version, sorry ) for SNPs called on 769 samples with 12x coverage HiSeq data. The median quality score is at ~Q750 and the mean at ~Q28000. I was just wondering if you could comment on how well calibrated these quality scores are and whether/how the number of samples and/or coverage would affect them?
Thanks in advance,