This repository is a component of ChromShatter designed for detecting somatic structural variants from BAM files. It is a modified version of Delly, adapted to fit the overall workflow of the ChromShatter algorithm.
You can build ChromShatter from source using a recursive clone and make.
git clone --recursive https://github.com/PPSherry/ChromShatter.git
cd ChromShatter/
make all
chromshatter call [OPTIONS] -g <ref.fa> <tumor.sort.bam> <normal.sort.bam> -o output.tsv
This command would output a .tsv file, which contain SV info and can be used in the SV visualization step.
ChromShatter is distributed under the BSD 3-Clause license. Consult the accompanying LICENSE file for more details.
Delly is a widely used bioinformatics tool for structure variant detection. HTSlib is heavily used for all genomic alignment and variant processing. Boost for various data structures and algorithms and Edlib for pairwise alignments using edit distance.