Dear all, 

in the light of a new article in PLOS : "Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data" (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0151664) that recommends the use of Mutect, Strelka and Virmid for somatic mutation calling, wondering if you guys can share your experience with these 3 algorithms, or if you have any other recommendations. Thanks a lot, 

bogdan   
I always interpret some of these results with a healthy grain of salt, in particular because the actual truth set of mutations usually isn't defined, so that there is no good analysis of Precision, Recall, and other measures. The authors also generally assumed that the four callers that had tended to converge on one another, and had the most agreement with each other, where also the correct callers. I happen to agree with them, but that kind of reasoning can be flawed if they are suffering from systematic bias due to a similar calling method. That said, of the recommended callers I've only used MuTect extensively. I'm somewhat surprised that FreeBayes wasn't included as it is widely considered to be an excellent Haplotype based caller as well. MuTect, in my experience, works quite well, although I've found getting the old version is now somewhat of a pain to find and download, and get good documentation for. There are also issues I believe with making sure you are using the correct Java version, which is a perennial problem for Java software in general and anything that uses the GATK in any way in particular.

I'm now looking at testing EBCall and Virmid in my own pipeline as they weren't in there. I've been using MuTect, FreeBayes, Scalpel, VarDict, Pindel, and Platypus.