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UnifiedGenotyper: metrics for quality score (and pics)

BlueBlue Posts: 17Member

I was wondering, in the vcf output from UnifiedGenotyper what metrics go into the variant quality score, QUAL ?

I'm assuming that depth, DP is one of them but I can't find further information. Apologies if I've missed it.

Attached are some plots of the depth and quality distribution for variant calls, and also of the relationship between depth and quality. I'm slightly worried that the bimodal quality distribution indicates an error, otherwise I've just attached the graphs for general interest.

gatk_ug_dp_qual1.png
1182 x 887 - 109K
gatk_ug_dp_qual2.png
1182 x 886 - 170K

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