chapmanb/bcbio-nextgen — pull request #688 by lpantano (2014-12-08 16:32:14+00:00)
Title: Add qsnp to paired tumor/normal samples

Hi,

I integrated qSNP to test it on paired samples.
Mainly problems were/are:
* the tool need a INI file, I create a dict withe default parameters, and then write it down as a file.
* the tools doens't accept BED files or region to target the analysis, so I needed to split BAM files as part of the function
* If a region is giving, and there is target file in the YAML file, I need to cross them and get the result of `bedutils.merge_overlaps`. If I got a tupple, then I continue with the anlaysis of one reigon. But if I get a BED file, I convert that to a list of tupple and do one region after another.
* the VCF ouput is a little mess, need to add FILTER and INFO annotation. As well, to replace some FILTER types, change sample names, and add REJECT when the variant is not somatic.

I tested with `run_info-cancer.yaml` and it worked, but don't have any positive data to check whether the filter function is realy working. The documentation is not clear about when the variant is somatic in the VCF file. I assumed, INFO has SOMATIC flag.

If you see something wrong or I can improve before testing, let me know, happy to modify anyting.

cheers