I'm trying to use ASCAT to assess CNV from Illumina Hiseq whole exome data.

Don't have reliable access to a windows computer at the moment, so I haven't been able to use genomestudio to determine BAF and LRR.

I'm pretty new to data analysis and am having a hard time figuring out which packages I need to use to pre-process the WES data for ASCAT.

Any recommendations for packages to use / a general pipeline for pre-processing the WES data for ASCAT?

Thanks