Merges similar SVs from multiple single sample VCF files. The tool was written for merging SVs discovered using Manta calls, but should support (almost) any SV VCFs. The output is a VCF file containing all merged SV sites (with no calls). The output can be given as input into GraphTyper to genotype the sites.
- Python 3.4+
- pysam
python3 svimmer input_vcfs chrA chrB chrC ...where input is a list of tabix indexed+bgzipped VCF files and chromosomes are the chromosomes to merge. For further details see the help page:
python3 svimmer -h
GNU GPLv3