Short pipeline that forks umi-processing to CNV-calling of targeted sequencing data. The calls are adjusted for tumor purity and ploidy. Uses cnvKIT for the CNV calling and PureCN to estimate tumor purity and chromosomal ploidy.

Input:

• umi-processing-style config file
• umi-processing until the vardict step

Output:

• vcf: directory containing purity and ploidy adjusted CNV-calls
• plots: scatterplots of CNV-calls