Implement ASCAT analysis for WGS data
The input is two BAM files, one from tumor and one from normal (blood) tissue and a given list of genomic positions. Output is several plots as well as copy number, BAF and other information for each of the given positions. There are also some summary statistics for average ploidy, normal cell contamination, etc.
Inspection of the final result is needed since there may be more than one possible solution and it should be possible to re-do the analysis with different starting values for the
A starting point for getting the software is the AscatNGS package https://github.com/cancerit/ascatNgs
There is a pre-build docker image (https://github.com/cancerit/dockstore-cgpwgs) that can be used as a template for a Singularity container. The ASCAT version is a bit old (2.5.1), but it should be possible to update this to the latest (3.1.2) in our Singularity build process. We need to apply some minor modifications to the wrapper scripts in the docker container.