Somatic copy number alterations for the
After individual samples are processed with the
wes route, manually define tumor-normal sample pairs in the
samples.pairs.csv sample sheet.
Add a BED file defining the genomic regions of the probes/baits to the project directory. The baited regions (or capture targets) are the loci your kit actually captures and should include flanking regions on either side of the targeted regions.
wes-pairs-cnv route from the same directory as