Software To Call Somatic Indels?

Question

[Jack]

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.

[Malachi Griffith]

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

Answer 1

[Chris Miller]

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

Answer 2

[Charles Warden]

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.).

[Jack]

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.

Answer 3

[Malachi Griffith]

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:

• Sensitive Long-Indel-Aware Alignment of Sequencing Reads
• DeNovoGear
• HaplotypeCaller

Answer 4

[Korsocius]

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.