CostelloJ-PSCN-Seq

Parent-specific copy number estimation pipeline.

Setup (once)

1. Run Rscript 0.setup.R once. This will setup links to shared annotation data sets and lab data files on the TIPCC compute cluster.
2. Make sure ./config.yml is correct. It specify the default analysis settings. The individual entries can be overridden by individual command-line options to the below Rscript calls.

Data processing

The following scripts should be run in order:

• Rscript 1.mpileup.R
• Rscript 2.sequenza.R
• Rscript 3.pscbs.R
• Rscript 4.reports.R

You may adjust ./config.yml when new files come in, or you can overridden the defaults individually via command-line options.