I want to benchmark somatic variant callers. The callers should:
- handle tumor/normal genomes, but it would be nice if the caller could handle exomes, targeted resequencing, etc
- be well supported and maintained (e.g. questions/answers regarding software being posted in online forums, bug fixes and new releases being released, etc)
- published in peer-reviewed journal (or at least in submission)
- output final results in VCF
Note that somatic SNPs is the main priority at the moment.
This older BioStars post has provided a very nice summary of tools available ~2 years ago:
A: Best Software For Detection Of Somatic Mutations From Matched Tumor:Normal Ngs D
Given my list of requirements, I've come up with these 14 tools:
Are there any others you would recommend?