How the GQ of a SNP is calculated by UnifiedGenotyper?

desmo · 02-06-2014, 12:21 AM

Hi, I'm trying to understand how does UnifiedGenotyper usually calculate the GQ of a SNP.
I understood the model to calculate the Likelihood of all the genotypes (AA,AC, AG,AT,CC,CG,CT,GG,GT,TT).

Once all the likelihood have been calculated, correct me if I'm wrong, the likelihood of the best genotype is normilized to 1 and all the other likelihoods are normilezed according to that scale.
So the PL field in the VCF should be the Phred-scaled values of the normalized values.

But is not clear to me how do they finally calculate the GQ value.
What values do they use to calculate that quality (normalized or phred scaled)? And what's the right formula?

I've tried to debug the code but it ends to be really tricky.
I really hope that anyone of you know the answer and would help me. I would be really thankfull for that.

Jeremy · 02-07-2014, 12:15 AM

The GATK forum would probably be a better place to ask this, the developers of GATK often reply to this sort of question.

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02-06-2014, 12:21 AM	#1
desmo Member Location: Pavia Join Date: Nov 2011 Posts: 25	How the GQ of a SNP is calculated by UnifiedGenotyper? Hi, I'm trying to understand how does UnifiedGenotyper usually calculate the GQ of a SNP. I understood the model to calculate the Likelihood of all the genotypes (AA,AC, AG,AT,CC,CG,CT,GG,GT,TT). Once all the likelihood have been calculated, correct me if I'm wrong, the likelihood of the best genotype is normilized to 1 and all the other likelihoods are normilezed according to that scale. So the PL field in the VCF should be the Phred-scaled values of the normalized values. But is not clear to me how do they finally calculate the GQ value. What values do they use to calculate that quality (normalized or phred scaled)? And what's the right formula? I've tried to debug the code but it ends to be really tricky. I really hope that anyone of you know the answer and would help me. I would be really thankfull for that.

02-07-2014, 12:15 AM	#2
Jeremy Senior Member Location: Pathum Thani, Thailand Join Date: Nov 2009 Posts: 190	The GATK forum would probably be a better place to ask this, the developers of GATK often reply to this sort of question.