Service Notice: Due to the blizzard currently hammering the US Northeast, the Broad is shut down and the GATK forum will be mostly unattended while we hunker down and sip hot cocoa with marshmallows. Assuming the power stays on and we're able to dig ourselves out of the snow when it's all over, normal service should resume Wednesday or Thursday.

Calibration of QUAL field emitted by the Unified Genotyper

LaurentLaurent Posts: 38Member, GSA Collaborator

Hi,

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, Laurent

Best Answer

Answers

Sign In or Register to comment.