./SURVIVOR ID

Program: SURVIVOR (Tools for Structural Variations in the VCF format)
Version: 1.0.3

Usage: SURVIVOR <command> [options]

Commands:
-- Simulation/ Evaluation
	simSV	Simulates SVs and SNPs on a reference genome.
	scanreads	Obtain error profiles form mapped reads for simulation.
	simreads	Simulates long reads (Pacio or ONT).
	eval	Evaluates a VCF file after SV calling over simulated data.

-- Comparison/filtering
	merge	Compare or merge VCF files to generate a consensus or multi sample vcf files.
	filter	Filter a vcf file based on size and/or regions to ignore
	stats	Report multipe stats over a VCF file
	compMUMMer	Annotates a VCF file with the breakpoints found with MUMMer (Show-diff).

-- Conversion
	bincov	Bins coverage vector to a bed file to filter SVs in low MQ regions
	vcftobed	Converts a VCF file to a bed file
	bedtovcf	Converts a bed file to a VCF file
	smaptovcf	Converts the smap file to a VCF file (beta version)
	bedpetovcf	Converts a bedpe file ot a VCF file (beta version)
	hapcuttovcf	Converts the Hapcut2 final file to a VCF file using the original SNP file provided to Hapcut2
	convertAssemblytics	Converts Assemblytics to a VCF file```