About Dream Challenge Somatic Mutation Calling Algorithms
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8.1 years ago
morovatunc ▴ 550

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?

Somatic-Mutations SNV DREAM • 1.8k views
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8.1 years ago
TriS ★ 4.7k

maybe this helps A: Variant Caller Of Choice?

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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.

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