Question: Best Software For Detection Of Somatic Mutations From Matched Tumor:Normal Ngs Data
19
gravatar for Travis
6.9 years ago by
Travis2.8k
USA
Travis2.8k wrote:

Hi all,

I know of various software solutions for this problem e.g. Somatic Sniper, JointSNVMix, etc., but having never used any of them, I am curious if any comparisons of their performance exist (peer-reviewed or otherwise).

Thanks in advance. 

ADD COMMENTlink modified 4.2 years ago by Malachi Griffith17k • written 6.9 years ago by Travis2.8k
45
gravatar for Malachi Griffith
5.9 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith17k wrote:

Here are a few more, a summary of the other answers, and updated links:

For a much more general discussion of variant calling (not necessarily somatic or limited to SNVs/InDels) check out this thread: What methods do you use for In/Del/SNP calling?

Some papers describing comparisons of these callers:

The ICGC-TCGA DREAM Mutation Calling challenge has a component on somatic SNV calling.

ADD COMMENTlink modified 3.1 years ago • written 5.9 years ago by Malachi Griffith17k
3

This paper used validation data to compare popular somatic SNV callers:

Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by Qingguo30
2

You can also use freebayes to call them. Specify --pooled-discrete and --genotype-qualities, call germline/somatic at the same time, and then pass the result through vcfsamplediff (vcflib).

ADD REPLYlink written 5.3 years ago by Erik Garrison2.1k

Virmid paper has been published in Genome Biology. Please enjoy. http://genomebiology.com/2013/14/8/R90/abstract

Note: Please read PDF version instead of the html full text. The publication team made a mistake to replace two figures with another :( It will be fixed soon anyway.

ADD REPLYlink modified 5.3 years ago • written 5.3 years ago by Sangwoo Kim340

Can Virmid call InDels? When I use Virmid, it only give me SNPs. And I didn't see any parameters that can allow me to call InDels.

ADD REPLYlink written 4.4 years ago by xieshaojun062190

You'll need to update the link to MuTect. Broad Institute has begun to put portable versions of their tools on Github, like the latest release of MuTect. The Genome Institute at WashU has been using Github for a while, but portable versions of their tools can be found here and here.

ADD REPLYlink modified 4.4 years ago • written 5.0 years ago by Cyriac Kandoth5.2k
16
gravatar for lh3
6.9 years ago by
lh331k
United States
lh331k wrote:

Perhaps you should read my samtools paper, where I did an experiment on finding rare differences between data from different sources but for the same individual.

In general, my view is as long as read placement is perfect, even naive methods work sufficiently well. Complex methods only give you theoretical comfort in that case. One of hard parts is all kinds of alignment artifacts. SNVMix and another paper published in Bioinformatics last year try to resolve this by machine learning using multiple statistics that may imply alignment errors. I, however, always prefer to tackle a problem directly, if we can, rather than via machine learning. To me, the simplest yet most effective strategy is to use two distinct alignment algorithms, such as bwa and bwa-sw, which have distinct error modes. You only consider mutations shared between the two alignments. False calls will be vastly reduced. Using decoy sequence also helps around centromeres.

Another complication is structural variations, in which I am less experienced. In some sense, false mutations caused by structural variations are still indication of something different between normal and tumor.

In all, I think you do not need to worry about which software to use for detecting somatic mutations - anything reasonable is fine. You should pay more attention to mismapping and structural variations. My sanger colleagues from the Cancer Group would agree with me. They have published many high-profile papers.

ADD COMMENTlink written 6.9 years ago by lh331k
4
gravatar for Obi Griffith
6.9 years ago by
Obi Griffith17k
Washington University, St Louis, USA
Obi Griffith17k wrote:

In this paper describing the HugeSeq pipeline they compare SNP detection from GATK and SamTools. And, also compare/combine a number of different methods for structural variation detection.

ADD COMMENTlink written 6.9 years ago by Obi Griffith17k
2
gravatar for Rm
6.9 years ago by
Rm7.8k
Danville, PA
Rm7.8k wrote:

We use varscan and SomaticSniper along with samtools and GATK

ADD COMMENTlink written 6.9 years ago by Rm7.8k

Hello, I am novice on SomaticSniper, bam-somaticsniper -q 1 -Q 40 -f ucsc.hg19.fasta ERR031023.bam ERR031024.bam ERR031024.snp.vcf, this is the command line I used to call different snps between one pair of cancer and normal samples. Unfortunately, I got a large number of machine artifact. May you send me your command line of Somaticsniper? Any suggestion is appreciated.

ADD REPLYlink written 6.1 years ago by jiagehao10
1
gravatar for Zev.Kronenberg
6.9 years ago by
United States
Zev.Kronenberg11k wrote:

I think you can now hand Samtools the tumor:normal data together. Also SNVer is worth a look. It uses a different model than Samtools.

ADD COMMENTlink written 6.9 years ago by Zev.Kronenberg11k
1
gravatar for Aeonsim
6.9 years ago by
Aeonsim10
NZ
Aeonsim10 wrote:

You could try these guys software http://www.realtimegenomics.com/Applications/Sequence-Analysis/Cancer-Research I've used there other tools (mapping, variant calling etc) in my work with Bovine sequence data but have not had any reason/chance to try out there tumor/control tools. I

f their tumor tool is anything like their other tools it should be very fast and rather sensitive. They're a free research license available which should be suitable for most researchers.

ADD COMMENTlink written 6.9 years ago by Aeonsim10
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