Biostar Beta. Not for public use.
Software To Call Somatic Indels?
3
Entering edit mode
6.2 years ago
Jack • 60

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 • 5.6k views
ADD COMMENTlink
0
Entering edit mode
ADD REPLYlink
2
Entering edit mode
14 months ago
Washington University in St. Louis, MO

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

ADD COMMENTlink
1
Entering edit mode
12 months ago
Duarte, CA

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
0
Entering edit mode

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
1
Entering edit mode
16 months ago
Washington University School of Medicin…

Many tools for detecting somatic SNVs are described here: https://www.biostars.org/p/19104/

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

ADD COMMENTlink
0
Entering edit mode
13 months ago
Korsocius • 110

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

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.1