[dpryan]

Ah, that can be am indicator of a few things, the most likely of which is that there's just a high level of PCR duplication in those regions. You can most easily check for this by opening the affected files in IGV or another viewer and just seeing if a disproportionate number of reads (or pairs) have the same start/stop bounds.

[id0]

Try increasing the --maxNumberOfReads argument for SomaticIndelDetector. That may be resolve your problem.

--maxNumberOfReads / -mnr ( int with default value 10000 )
Maximum number of reads to cache in the window; if number of reads exceeds this number, the window will be skipped and no calls will be made from it.

[jp.]

Thank you dpryan and id0,
Oh..However, I have used picard but still PCR duplicates ?
I will try use id0's recommendation.
There are two more problems I have after this:
1. I have converted .vcf output of SomaticIndelDetector using convert2annovar.pl. However, I am confused with MuTect .wig.txt out to convert so that I can use it as a In-put file for Annovar ?
2. MuTect can run without control samples using only tumor . SomaticIndelDetector does not work without control sample.bam. It asks minimum 2 samples. My case samples are from cell lines, there is no control or normal. How can I use SomaticIndelDetector ? I studied few articles and googled but can not understand. Can somebody explain me please ?
Thank you in Advance.