This pacakge is designed to take MANTA or SvABA VCF files which have been run without a paired normal and classify each rearrangement as germline or somatic.
- This has been tested on the current versions of OSX, Linux, Ubuntu, Windows (as of April 1, 2022)
- Install R-4.0 or newer (https://www.r-project.org/)
- Install necessary packages
install.pacakges('devtools')
install.packages('parallel')
install.packages('BiocManager')
library(BiocManager)
BiocManager::install('GenomicRanges')
library(devtools)
devtools::install_github('mskilab/gUtils')
Documentation for these packages can be found at:
devtools
parallel
BiocManager
GenomicRanges
gUtils
- Install InProgress
Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS=TRUE)
devtools::install_github('acranej/InProgress')