Question: About Dream Challenge Somatic Mutation Calling Algorithms
gravatar for morovatunc
3.2 years ago by
morovatunc400 wrote:


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 challlange is harder in somatic mutations than gremline 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 subchallange #2,#3 and #4 in Strucutral 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 dont 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 ?

snv somatic mutations dream • 1.0k views
ADD COMMENTlink modified 3.2 years ago by TriS3.6k • written 3.2 years ago by morovatunc400
gravatar for TriS
3.2 years ago by
United States, Buffalo
TriS3.6k wrote:

maybe this helps A: Variant Caller Of Choice?


ADD COMMENTlink written 3.2 years ago by TriS3.6k

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.

ADD REPLYlink written 3.2 years ago by morovatunc400
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1001 users visited in the last hour