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

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 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
0
gravatar for TriS
3.2 years ago by
TriS3.6k
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
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