Hi,
I have to do mutational calling to ICGC and TGCA for given specific regions. For that purpose, I have been trying to find the best software which can reveal indels and other somatic mutations. I am aware of why this challenge is harder in somatic mutations than germline mutations in terms of Variant Allele Frequency etc.
I checked the leaderboards of DREAM challenge and I could only find SomaticSeq algorithm published in the literature out of it.
Biggest advantage of somaticseq, since it is an ensemble approach it combines 5 algorithms from the literature. Which give slightly better results. However, there are other algorithms such as novoBreak which was the leader of subchallenge #2,#3 and #4 in Structural variations category and one algorithm from Washington University in SNV category. Also there is carcerevo which performed as good as somaticseq. How can I find these algorithms ? Could you guys suggest me a way?
There is nothing against to SomaticSeq but I don't wanna rely on a single algorithm. Also, Could you guys give some ideas about possible alternatives and ensemble approach vs single sole algorithm in terms of efficiency and performance?
That one helps but as you may understand from the question, I asked specifically about recent algorithms such as SomaticSeq. Just published couple months ago. However, I will definitely take a look at that post. Thank you.