SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Zygosity in Indel Calling Jeromek Bioinformatics 0 09-15-2014 10:04 AM
CNV and INDEL calling Nilaksha Genomic Resequencing 2 05-05-2014 09:15 PM
NEWBIE: What is relation between SNP calling, INDEL calling and Genotype calling? arkilis Bioinformatics 4 10-01-2013 06:57 PM
SNP and indel calling methods Rachelly Bioinformatics 1 11-24-2010 04:45 AM

Reply
 
Thread Tools
Old 09-30-2015, 04:50 PM   #1
ndelaney
Member
 
Location: Cambridge, MA

Join Date: May 2011
Posts: 19
Default Papers Describing Indel Calling Algorithms

Does anyone happen to know where I could find detailed information on the algorithms used to call indels and assign confidence for the following programs:

* GATK
* SAMTOOLS
* Vardict
* FreeBayes

I gather some of the publications out there are out of date.
ndelaney is offline   Reply With Quote
Old 10-04-2015, 03:43 PM   #2
Len Trigg
Registered Vendor
 
Location: New Zealand

Join Date: Jun 2011
Posts: 29
Default

If you are interested in the algorithms behind indel calling in general, the method used by RTG Core for indel calling (and complex haplotype calling) is described in: http://www.ncbi.nlm.nih.gov/pubmed/24874280
__________________
Len Trigg, Ph.D.
Real Time Genomics
www.realtimegenomics.com
Len Trigg is offline   Reply With Quote
Reply

Tags
gatk, indel analysis, samtools, vardict

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 03:38 AM.


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