SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
how to identify SNPs and indels between two samples pandafengye Genomic Resequencing 3 08-29-2013 05:57 AM
find all snps/indels prbndr Bioinformatics 2 09-20-2011 10:43 AM
how to validate SNPs and Indels after assembly? sulicon Bioinformatics 9 02-25-2011 04:27 AM
1KG SNPs and Indels file mpiro Bioinformatics 4 01-31-2011 03:55 AM
Software for Sorting SNPs/ InDels by Affect? Nix Bioinformatics 2 10-27-2010 02:24 PM

Reply
 
Thread Tools
Old 08-16-2012, 10:31 AM   #1
skblazer
Member
 
Location: Massachusetts

Join Date: Feb 2009
Posts: 50
Default Calling SNPs and InDels simultaneously or seperately?

Hi,

I want to know when call variants by GATK pipeline, you call SNPs and InDels simultaneously (use -glm BOTH) or separately in two rounds of run. I noticed that considering BAQ will decrease the performance of calling InDels. But how can I deal with the conflicted alleles generated by SNPs and their nearby InDels?

Best,
SK
skblazer is offline   Reply With Quote
Reply

Tags
indel snp

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 10:07 AM.


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