SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How is the p-value for MAPQ calculated in Bowtie2? Cameron MacPherson Bioinformatics 0 03-22-2013 08:17 AM
SNP calling using GATK UnifiedGenotyper baika Bioinformatics 1 02-25-2013 02:41 PM
GATKv2 UnifiedGenotyper SNP heterozygosity are extremely high!!! SD2010Bioinfo Bioinformatics 0 12-11-2012 01:10 AM
GATK UnifiedGenotyper SNP calling with Agilent 50Mb target enrichment nullalleles Genomic Resequencing 1 07-18-2011 07:28 AM
How is SNP quality calculated in SAMTOOLS pileup? lazyworm Bioinformatics 2 05-28-2010 01:00 AM

Reply
 
Thread Tools
Old 02-06-2014, 12:21 AM   #1
desmo
Member
 
Location: Pavia

Join Date: Nov 2011
Posts: 25
Default 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.
desmo is offline   Reply With Quote
Old 02-07-2014, 12:15 AM   #2
Jeremy
Senior Member
 
Location: Pathum Thani, Thailand

Join Date: Nov 2009
Posts: 190
Default

The GATK forum would probably be a better place to ask this, the developers of GATK often reply to this sort of question.
Jeremy is offline   Reply With Quote
Reply

Tags
genotype, unifiedgenotyper, vcf

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:09 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO