InProgress Overview

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.

System Requirements and Dependencies

• This has been tested on the current versions of OSX, Linux, Ubuntu, Windows (as of April 1, 2022)

Installation

1. Install R-4.0 or newer (https://www.r-project.org/)
2. 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

3. Install InProgress

Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS=TRUE) 
devtools::install_github('acranej/InProgress')