IndelRealigner on fragment data

[jcgrenier]

Hi everyone,

I want to locally realign some bam files coming from exome fragment data with the GATK IndelRealigner tool. I have done the same with some data coming from exome paired-ends and found what I was looking for (candidate variants used for indel calling).

The problem reside in the fact that when I realign fragment data with this tool, I found pretty much less candidate variants than with the fragindel tool in bioscope.

Also, I've visualized the bam files without PCR duplicates, the one coming from fragindel (bioscope) and the other coming from IndelRealigner from GATK and another which is a bam directly coming from the mapping step in bioscope, and found that there's a part of the reads, where there are indels that I don't call, with the realigned bam that are hidden in the two last bam.

Do you have an idea about what can cause this problem? And do you know if I can realign exome fragment data with GATK?

Thanks a lot.

[jcgrenier]

I found what was going on. I had to prepare the bam file before running the IndelRealigner. I thought that the IndelRealigner was able to find the indels but I had to run the smallfragIndel tool first and then realign the bam it gave me!