SurVTyper

A genotyper for structural variations using NGS paired-end sequencing data.

Installation

Download and uncompress the latest release. From inside the folder, run

./build_htslib.sh
cmake -DCMAKE_BUILD_TYPE=Release . && make

Running

SurVTyper needs a VCF file with the SVs to genotype, BAM/CRAM file, a (possibly empty) working directory and reference genome in FASTA format.

The command for running it is:

python3 survtyper.py --threads N_THREADS VCF_FILE BAM_FILE WORKDIR REFERENCE

The genotyped VCF will be placed in WORKDIR/genotyped.vcf.gz.