SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
PostDoc: Genomics, Epigenomics & Transcriptomics of Bacterial & Eukaryotic Pathogens vxtecom Academic/Non-Profit Jobs 0 03-22-2016 08:43 PM
Using GATK's local realigner outside of GATK pipeline for variant calling NikTuzov Bioinformatics 1 09-08-2015 08:41 AM
BWA & GATK parallel parameters. jofe Bioinformatics 0 08-28-2013 05:44 AM
SOlid &&&& Metagenomics fanyucai1 Metagenomics 7 01-21-2013 09:08 PM
Default quality encoding system of SAMTools&GATK dingxiaofan1 Bioinformatics 11 03-03-2011 11:27 PM

Reply
 
Thread Tools
Old 04-26-2019, 10:29 AM   #1
rajitz
Junior Member
 
Location: Toronto

Join Date: Apr 2019
Posts: 1
Default GATK GermlineCNVCaller & PostprocessGermlineCNVCalls

Hi, I was wondering if anyone here has experience in running GATK GermlineCNVCaller & PostprocessGermlineCNVCalls for calling CNVs in germline samples?

The VCF files that I'm getting always have ALT to be "<DEL>,<DUP>". Shouldn't ALT be just one of them or neither? Somehow both the interval and segment VCF files I'm looking at have all positions marked as "<DEL>,<DUP>".

If anyone here has experience with this, I would really appreciate some feedback. Thanks!
rajitz is offline   Reply With Quote
Reply

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 04:59 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO