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.