Question: single sample somatic variant calling software
gravatar for Zhenyu Zhang
3.0 years ago by
Zhenyu Zhang250
United States
Zhenyu Zhang250 wrote:

There are many softwares that can call tumor normal pairs easily. However, in a real clinical setting, we only have tumor sample, and likely on FFPE slides.

Does anyone have any suggestions one single tumor sample variant calling pipelines without normals? I know some softwares like MuTect do have single sample mode, but likely to have many junks b/c it's not designed to do so. I am looking for more complicated tools, like the one FoundationOne is using.

ADD COMMENTlink modified 21 months ago by daniel30 • written 3.0 years ago by Zhenyu Zhang250
gravatar for igor
3.0 years ago by
United States
igor8.1k wrote:

MuTect has a "panel of normals" option (--normal_panel argument), so you can compare to a group of normal samples. This cleans up the results significantly. See the "Normal-only calling for panel of normals creation" section at

FoundationOne is doing something similar to that. However, it is not as sophisticated as you think. I once checked tumor and matched normal tissue for a patient who also had FoundationOne results without a matched normal. More than 90% of FoundationOne highlighted variants turned out to be not really somatic. This was a couple of years ago and they surely improved their process, but there is only so much room for improvement.

You can also check against other databases such as 1000 Genomes or ExAC for population allele frequencies.

However, calling somatic variants without a normal is not a good idea even though you can publish them in reputable journals.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by igor8.1k

There is a new paper from Shi et al. that summarizes this well:

Cancer-only WES pipelines are unreliable (69% somatic mutations are false positive)

ADD REPLYlink written 9 months ago by igor8.1k
gravatar for tamsen
3.0 years ago by
tamsen20 wrote:

Hi Shakuras,

You are welcome to try Pisces. We use it extensively for single-sample FFPE samples.

Get 5.1.3 branch or binary for now. Should have a new release posted in a few weeks.

ADD COMMENTlink written 3.0 years ago by tamsen20

OK, that took a while. 5.1.6 is now released.

ADD REPLYlink written 2.7 years ago by tamsen20
gravatar for tim.chu90
3.0 years ago by
tim.chu900 wrote:

Our lab has been working on something like this. It's still pretty new and is only works on a cluster, but if you're willing to try it we'd be happy to work with you to get it working. Feel free to PM me if you're interested.

ADD COMMENTlink written 3.0 years ago by tim.chu900

Can you briefly explain how it works? The tool is well-documented, but there isn't a lot of background info (unless you want to go through the source code). It says it's using machine learning, so that assumes that certain features make a mutation more or less likely to be somatic. What are they?

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by igor8.1k
gravatar for de.subhajyoti
2.9 years ago by
United States
de.subhajyoti10 wrote:

You can also try SomVarIUS. It is developed for somatic variant identification from unpaired tissue samples. The link to the publication is: and the software can be found at

ADD COMMENTlink written 2.9 years ago by de.subhajyoti10
gravatar for daniel
21 months ago by
United Kingdom
daniel30 wrote:

Octopus is capable of tumour only somatic and germline variant calling. There is an evaluation of tumour-only calling on WGS data in the Octopus paper.

ADD COMMENTlink modified 9 months ago • written 21 months ago by daniel30
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