SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
gatk indel calling problem Alex Renwick Bioinformatics 6 12-02-2011 12:25 PM
- N options with maq 0.7.1 seq_GA Bioinformatics 1 10-21-2011 04:14 AM
SNP and indel calling methods Rachelly Bioinformatics 1 11-24-2010 04:45 AM
Tophat options to report unaligned reads and controlling Bowtie options Siva Bioinformatics 0 10-15-2010 08:38 PM
Novoalign options Gen2007 Bioinformatics 4 09-28-2010 09:34 PM

Reply
 
Thread Tools
Old 08-24-2011, 11:29 AM   #1
Hkins552
Member
 
Location: Baltimore MD

Join Date: Jun 2011
Posts: 18
Question Good Indel Calling Options?

Hi All,
I've found some dated posts regarding indel calling options in GATK, samtools, dindel, etc. What are the most current and suggested pipelines for indel calling?
Thanks!
Hkins552 is offline   Reply With Quote
Old 08-24-2011, 01:33 PM   #2
swbarnes2
Senior Member
 
Location: San Diego

Join Date: May 2008
Posts: 912
Default

Dindel is generally considered the best. But I've found up to 7-base indels fine with samtools and bwa.
swbarnes2 is offline   Reply With Quote
Reply

Tags
indel

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 11:47 PM.


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