Look for somatic mutation from Ion Proton Exome Sequencing

lethalfang · 10-23-2013, 03:38 PM

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!

sophiespo · 12-01-2013, 01:53 AM

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)

dakl · 09-11-2014, 02:42 AM

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

BR
daniel

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10-23-2013, 03:38 PM	#1
lethalfang Member Location: San Francisco, CA Join Date: Aug 2011 Posts: 91	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!

12-01-2013, 01:53 AM	#2
sophiespo Member Location: australia Join Date: Apr 2013 Posts: 15	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)

09-11-2014, 02:42 AM	#3
dakl Member Location: sweden Join Date: May 2009 Posts: 15	@sophiespo Any results from that exercise? What worked best for you in the end? Would be interested to hear. BR daniel