Skilifting PACT data

[shihabdider]

This issue involves creating appropriate data inputs from PACT raw data for viewing on case-reports.

@kevinmhadi will post the list of plots we expect to be able to view on case-reports given the PACT data we currently have (e.g metadata, coverage, hetsnps, etc.)

@shihabdider will ready skilift for converting raw output files into JSONs/arrows and then pair with @kevinmhadi to convert the outputs and build a PACT case-reports instance.

[kevinmhadi]

So in summary:

• Copy number track (total + allelic from the facets__pact column)
• SNV/Indel track + oncotable
• Possible QC, although I might need to provide custom Picard outputs for metrics
• Possible total and hetsnp coverage track (we would have to run our own pipeline for this on the bams we got)

Unfortunately, they didn't provide coverage, we can try running fragcounter + hetpileups and see if we can input those.