Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
mpileup and homozygous snps grievous Bioinformatics 5 02-19-2014 05:58 PM
homozygous and heterozygos asankaf General 15 04-04-2013 03:03 PM
Homozygous Ref calls and no calls ashkot Bioinformatics 1 08-09-2012 11:01 AM
Homozygous mammal sequence data dansullivanblk Bioinformatics 2 02-02-2012 04:36 AM
How to detect homozygous SNPs with GigaBayes fikys Bioinformatics 2 12-11-2009 07:00 PM

Thread Tools
Old 08-09-2012, 11:11 AM   #1
Location: Tennessee

Join Date: Jun 2012
Posts: 10
Default GATK, Homozygous Ref and GQ

When I force GATK to call SNPs that are homozygous for the reference, it fails to provide a GQ. I realize that the GQ is dependent on an estimation of the frequency of the alternate, which doesn't make too much sense for monomorphic sites, but we want to use GQ as a filter for valid calls, since GQ and QUAL are so different.

Version 1.0 of GATK did provide this information, but apparently that changed as they fixed some bugs.

Does anyone know of a trick to get GATK to produce the GQ for those sites? If not, what do folks who need to know that a homozygous for reference call is valid (such as when you are comparing blood calls with tumor base counts).
etorstenson is offline   Reply With Quote

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 07:28 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO