This package contains a collection of functions to explore breakpoint data produced by svParser i.e. the all_bps.txt or all_bps_filtered.bps files. Input to svBreaks should contain the following information:
event bp_number sample genotype chrom1 bp1 gene1 feature1 chrom2 bp2 gene2 feature2 type length(kb)
1 bp_1 A373R11 germline_recurrent 2L 73837 galectin exon_2 2L 73896 galectin exon_2 DEL 0.1
This tool is under constant development. Please feel free to contact me, or raise an issue if you encounter any problems.
Install from github:
git clone https://github.com/nriddiford/svBreaks.git
Start an R session, and install package:
library(devtools)
install_github("nriddiford/svBreaks")
library(svBreaks)