Question: calling somatic mutations on ion proton data
gravatar for CHANG
5.7 years ago by
United States
CHANG40 wrote:

I am trying to use Mutect to call somatic mutations on tumor/match normal pairs generated by ion proton ampliseq. However, none of the mutations pass mutect filter. I decided to take a lot at IGV to see to see if there's some quality issue and notice a lot of insertions in the read. Attached is a screen shot. Att

I am guessing all these insertions is making it difficult to call mutations. So I'm thinking the following solutions

1) Re-map with another aligner (i.e. BWA) and re-align with GATK

2) Adjust TMAP settings. I'm currently using Version 4.0-6 with default settings

3) Come up with some filtering steps for processing Ion Var caller output.

Does anyone have suggestions for calling somatic mutations on proton data?

Thank you.


ADD COMMENTlink modified 5.5 years ago by Bontus80 • written 5.7 years ago by CHANG40
gravatar for Bontus
5.5 years ago by
Bontus80 wrote:

Dear Chang,

As far as I know, Torrent Suite produces two separate variant calls after TMAP, at least that is what I received from our sequencing provider and they have used only Proton software. Thus, you should check whether there is a separate TS option that returns somatic variants prior to variant calling. Otherwise, re-mapping all reads and then running a different tool is of course also an option, however, since you already noticed the homopolymer issue in IGV, this might not make a big difference (TMAP is performing on par if not better than other aligners for Proton), so adjusting Mutect settings may be the better choice here.


ADD COMMENTlink written 5.5 years ago by Bontus80
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