Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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,