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.
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?