nf-core
ASCAT WES reference resources
Description of feature
Hi Developers,
I'm trying to run the Sarek implemented ASCAT for CNV analysis on WES data. On the nfcore Sarek website, it's suggested to follow 5 steps, as specified in this doc https://nf-co.re/sarek/3.4.0/docs/usage#how-to-generate-ascat-resources-for-exome-or-targeted-sequencing, to generate reference information (allele.zip, loci.zip, GC.zip, and RT.zip) for exome data instead of using the default igenome directly. I noticed that the ASCAT author had also provided ref files for WES at https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WES, which seemed to be a ready-to-use version when provided with an appropriate BED file. Would it be feasible to replace the default ignome ref with those for Sarek ASCAT?
I'm now running Sarek with params (-- --ascat_alleles, --ascat_loci, --ascat_loci_gc, --ascat_loci_rt) on the command line. The pipeline seems to work well. But, it would be great to hear advice from you.
Thank you!
