Missing a indel from targated sequencing

[Rajesh Patidar]

Hi,

I have a sample where we did exome as well as Panel and there is one Indel which is called in exome but not called in panel seq at all. its not even in all.somatic.indels.vcf

the input bam file for tumor and normal all have good coverage in Exome (>400X) and >700X in Panel, the indel is found to be at 13% in Exome and ~10% of reads show the same in panel sequencing.

Could you please suggest what should I do here. 

I could send you the portion of bam files for the position if that helps investigating it further.

Thanks a lot.

Rajesh

[Sean Davis]

Hi, Rajesh.

Silly question, but did you disable depth filters in both cases?  And just so the list knows, what version of Strelka are you using?

Sean

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Sean Davis, MD, PhD

Center for Cancer Research

National Cancer Institute

National Institutes of Health

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[Rajesh Patidar]

my maxInputDepth =10000

you can see whole config file here https://github.com/patidarr/ngs_pipeline/blob/master/Tools_config/TGen_Strelka.config.ini

Strelka version 1.0.14

On Thursday, April 6, 2017 at 9:05:06 AM UTC-4, Sean Davis wrote:

Hi, Rajesh.

Silly question, but did you disable depth filters in both cases?  And just so the list knows, what version of Strelka are you using?

Sean

On Thu, Apr 6, 2017 at 8:30 AM, Rajesh Patidar <rajbtp...@gmail.com> wrote:

Hi,

I have a sample where we did exome as well as Panel and there is one Indel which is called in exome but not called in panel seq at all. its not even in all.somatic.indels.vcf

the input bam file for tumor and normal all have good coverage in Exome (>400X) and >700X in Panel, the indel is found to be at 13% in Exome and ~10% of reads show the same in panel sequencing.

Could you please suggest what should I do here. 

I could send you the portion of bam files for the position if that helps investigating it further.

Thanks a lot.

Rajesh

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