SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Question about the concordance between GATK and Samtools sunbert Bioinformatics 4 03-01-2013 10:10 PM
Little concordance between GATK and Samtools ramirob Bioinformatics 5 07-18-2012 12:47 AM
indel caller - GATK or Pindel, or anything else? caswater Bioinformatics 0 06-28-2012 11:11 AM
concordance between GATK and Samtools caswater Bioinformatics 6 06-06-2012 12:42 AM

Reply
 
Thread Tools
Old 06-07-2017, 03:51 AM   #1
JSThompson
Junior Member
 
Location: Cambridge, UK

Join Date: Jun 2017
Posts: 4
Default Pindel and GATK AD Concordance

I was hoping to get some advice on working with the AD field for variants in VCFs produced by Pindel and Pindel2VCF.

My lab has a variant calling pipeline that uses GATK's UnifiedGenotyper for calling SNVs and small Indels, as well as using Pindel to call deletions and short insertions. As part of our VCF filtering, we remove variants with an Variant Allele Fraction below a certain threshold. However, it has been brought to my attention by other members of the lab that when Pindel and UnifiedGenotyper call the same variant, they have different AD values and so different VAF values (I'm not sure if it's relevant, but the AD for UnifiedGenotyper is the same as found in IGV).

Normally the difference is small enough that it doesn't affect our filtering, but there have been some cases where a variant called by both branches of the pipeline has an VAF greater than our cutoff threshold in one VCF, but has an VAF lower than threshold in the other VCF. To avoid this issue, which value for AD should I be using for calculating VAF? The AD from UnifiedGenotyper, or the AD from Pindel?

Thanks in advance for any suggestions.
JSThompson is offline   Reply With Quote
Old 06-08-2017, 05:34 AM   #2
JSThompson
Junior Member
 
Location: Cambridge, UK

Join Date: Jun 2017
Posts: 4
Default

I've also posted this thread on BioStars (https://www.biostars.org/p/256882/)
JSThompson is offline   Reply With Quote
Reply

Tags
depth of coverage, gatk, pindel, vaf

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 01:04 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO