Hello to all,
I am working with whole genome sequence data to call copy number variant. I want to use purity and ploidy aware copy number caller, so, I chose PureCN for this. I downloaded the PureCN package from the official website. Now to start working with my data, I need to generate a basic interval file from a BED file containing target coordinates and the command for this is:
$ export PURECN="/path/to/PureCN/extdata"
$ Rscript $PURECN/IntervalFile.R --infile baits_hg19.bed --fasta hg19.fa --outfile baits_hg19_gcgene.txt
When I run this command '$PURECN//IntervalFile.R': No such file or directory. Please help me with this issue. Also, I searched for this code manually in package folder, but I could not find any such code. Please, help.
Thanks in advance!