chapmanb/bcbio-nextgen — pull request #602 by lpantano (2014-09-22 14:07:32+00:00)
Title: pindel integration

Hi,

I added pindel as option for `indelcaller` and it will only work inside `mutect`. It is working with `tests` of paired tumor/normal, and tumor alone.

The only thing I missing is that it needs to know the `insert size` of the fragments. For now, I use 250, that more or less, is the one for illumina. Don't know if there is any function to get that value already integrated in bcbio.

It can be added as structural variant caller, but since the idea was to test indels first, just working as this, but can easily be moved to a general function.

Just let me know if there is a better way to integrate it. I just use `scalpel` as template for the code.

Didn't change docs because not sure if we will keep or not. But I can add it, if you think is the moment.