SURVIVOR

NAME

SURVIVOR - <short_description>

SYNOPSIS

SURVIVOR <command> [options]

DESCRIPTION

Program: SURVIVOR (Tools for Structural Variations in the VCF format) Version: 1.0.6

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.

genComp Generates a pairwise comparison matrix based on any multi sample VCF file filter Filter a vcf file based on size and/or regions to ignore stats Report multiple 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 to 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

AUTHOR

This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.