Question: Somatic indel calling with Pindel
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gravatar for sichan
2.4 years ago by
sichan50
Canada
sichan50 wrote:

Hello,

I noticed that Pindel was previously reported to not be able to call somatic indels without post-processing, e.g. see these posts:
Pindel Somatic Calls?
http://seqanswers.com/forums/showthread.php?t=42881

However, I noticed that the latest version of Pindel (0.2.5b1) has the --NormalSamples option.  According to the usage prompt, this flag turns on germline variant filtering:

-N/--NormalSamples
Turn on germline filtering, less sensistive and you may miss somatic calls (default false)

I run Pindel as follows:
pindel -f hg19.fa -i bam_config_file.txt -o Test1 --NormalSamples

My bam configuration file looks like:
/path/to/tumor/bam  insert_size Tumor
/path/to/normal/bam insert_size Normal

However, I noticed that the output still contains germline indels.  So perhaps the --NormalSamples hasn't been fully implemented yet and I'll still need to post-process results to get somatic indels from Pindel?

Thanks for any suggestions.

somatic pindel indels • 1.2k views
ADD COMMENTlink written 2.4 years ago by sichan50
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