Question: Software To Call Somatic Indels?
3
gravatar for Jack
6.1 years ago by
Jack70
Jack70 wrote:

I'm looking for a tool to call somatic indels (10-1000bp range, not point mutations) in tumor/normal samples. It looks like GATK doesn't support SomaticIndelDetector or Indelocator anymore. What tools are you using to call somatic indels? Are they well supported?

Thanks.

somatic cancer • 5.9k views
ADD COMMENTlink modified 2.3 years ago by Korsocius150 • written 6.1 years ago by Jack70

Relevant post: What Approach Would You Recommend For Large Indel Detection With Solid Data

ADD REPLYlink modified 5 months ago by RamRS27k • written 6.1 years ago by Malachi Griffith18k
2
gravatar for Chris Miller
6.1 years ago by
Chris Miller21k
Washington University in St. Louis, MO
Chris Miller21k wrote:

Pindel is another generally good somatic indel caller: http://gmt.genome.wustl.edu/pindel/current/

ADD COMMENTlink written 6.1 years ago by Chris Miller21k
1
gravatar for Charles Warden
6.1 years ago by
Charles Warden7.7k
Duarte, CA
Charles Warden7.7k wrote:

VarScan2 can call somatic indels (although they will be on the smaller side of the range you specified). It is also capable of making somatic copy number calls, which will be much larger.

If you use a tool to calculate read coverage, then you can also use log2ratio values for tumor versus normal samples using DNAcopy. This is the strategy I would lean towards for larger indels, but I've only done this with exome data (for example, I don't know if you are working with whole genome sequencing data, etc.).

ADD COMMENTlink written 6.1 years ago by Charles Warden7.7k

I work with exome sequencing data and I do use VarScan for CNV analysis. It works pretty well. As you commented, this is a good stragey for larger indels, perhaps a kilobase or larger... Smaller/weaker calls could get smoothed out by DNAcopy.

I need a caller that works between the ranges of a point-mutation caller and a CNV caller. I'm going to give Pindel a try.

Thanks a lot for your reply.

ADD REPLYlink written 6.1 years ago by Jack70
1
gravatar for Malachi Griffith
6.1 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith18k wrote:

Many tools for detecting somatic SNVs are described here: Best Software For Detection Of Somatic Mutations From Matched Tumor:Normal Ngs Data

Many/most of these tools will also detect small indels (< 10 bp), a few may detect larger indels in the range you describe.

A few more relevant items:

ADD COMMENTlink modified 5 months ago by RamRS27k • written 6.1 years ago by Malachi Griffith18k
0
gravatar for Korsocius
2.3 years ago by
Korsocius150
Korsocius150 wrote:

Really good and robust tool is CNVkit. py, but it is separate from somatic calling. I am using a samtools.. | varscan somatic and in other branch CNVkit, ther are some limitations, but it is work well.

ADD COMMENTlink written 2.3 years ago by Korsocius150
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