Tools used to apply QDNASeq R package to our P. falciparum data, including forging a BSGenome package.
Starting with a small R program , plus the seed file and shell commands to make the background data needed.
Added the file of centromere and telomere regions for blacklist.
Uploaded new version May 2017 that uses QDNAseq v1.10.0 . This version removed the need for several work-arounds previously required for P. falciparum data.
Code is example only; it is not free-standing. It has many local file names hard-coded, and reads file paths from a file which is not included.