8 weeks ago by
Sanger Institute, Cambridge, UK
Hello. dNdScv, which I developed, supports GRCh38. Although it uses hg19 by default, the package contains the files and instructions to run GRCh38, as well as functions to run it on any assembly or species. In benchmarking analyses by PCAWG (the ICGC/TCGA pancancer analysis of whole genomes consortium) dNdScv was shown to perform very similarly to MutSigCV in terms of specificity and sensitivity.
dNdScv is an R package. To install it you have to use:
To run driver discovery on GRCh38, you need to download the precomputed database for GRCh38, and then use:
dndsout = dndscv(mutations, refdb="RefCDS_human_GRCh38.p12.rda", cv=NULL)
See the tutorials above for more details if you are interested in the method.