SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Sort of a noob here: looking for somatic mutation in tumors (NGS sequencing) lethalfang Bioinformatics 8 10-06-2013 11:08 PM
hybridization failure- Target exome sequencing Ion proton vandy Ion Torrent 2 07-30-2013 02:12 AM
Library prep kits for Ion PGM or Ion Proton Bioo Scientific Vendor Forum 0 02-18-2013 06:25 AM
Ion Torrent $1000 Genome!? Benchtop Ion Proton Sequencer aeonsim Ion Torrent 88 10-28-2012 04:50 AM

Reply
 
Thread Tools
Old 10-23-2013, 02:38 PM   #1
lethalfang
Member
 
Location: San Francisco, CA

Join Date: Aug 2011
Posts: 91
Default Look for somatic mutation from Ion Proton Exome Sequencing

I've used Strelka and MuTect to find somatic mutations in SOLiD and Illumina data. They worked pretty well, but not so well for Ion Proton Exome (yes, a ton of homopolymer deletions and even more senseless insertions).

Does anyone have experience with somatic variant calling from Ion Proton or Ion Torrent?

Thanks in advance!
lethalfang is offline   Reply With Quote
Old 12-01-2013, 12:53 AM   #2
sophiespo
Member
 
Location: australia

Join Date: Apr 2013
Posts: 15
Default

I am currently in the process of validating a bunch of somatic mutations I detected in some exomes using MuTect and some other algorithms. I've been doing extensive research into the tools available for several months - some programs will under call (I've found that mutect severely under calls) and some will over call..

You'll find more problems with the indels rather than the SNVs.. The good news is that indel calling with a program like VarScan2 is not missing the true positives, you just get a ton of false positives and it's hard to differentiate between them.

(Sorry - only just saw this post)
sophiespo is offline   Reply With Quote
Old 09-11-2014, 01:42 AM   #3
dakl
Member
 
Location: sweden

Join Date: May 2009
Posts: 15
Default

@sophiespo
Any results from that exercise? What worked best for you in the end? Would be interested to hear.

BR
daniel
dakl is offline   Reply With Quote
Reply

Tags
exome, ion proton, ion torrent, proton

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 01:39 PM.


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