tools module

mavis.tools.SUPPORTED_TOOL = MavisNamespace(BREAKDANCER='breakdancer', BREAKSEQ='breakseq', CHIMERASCAN='chimerascan', CNVNATOR='cnvnator', DEFUSE='defuse', DELLY='delly', MANTA='manta', MAVIS='mavis', PINDEL='pindel', STARFUSION='starfusion', STRELKA='strelka', TA='transabyss', VCF='vcf')

Supported Tools used to call SVs and then used as input into MAVIS

mavis.tools.convert_tool_output(fnames, file_type='mavis', stranded=False, log=<mavis.util.Log object>, collapse=True, assume_no_untemplated=True)[source]

Reads output from a given SV caller and converts to a set of MAVIS breakpoint pairs. Also collapses duplicates