.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH SURVIVOR "1" "September 2020" "SURVIVOR 1.0.6" "User Commands"
.SH NAME
SURVIVOR \- <short_description>
.SH SYNOPSIS
.B SURVIVOR
\fI\,<command> \/\fR[\fI\,options\/\fR]
.SH DESCRIPTION
Program: SURVIVOR (Tools for Structural Variations in the VCF format)
Version: 1.0.6
.PP
Commands:
\fB\-\-\fR Simulation/ Evaluation
.TP
simSV
Simulates SVs and SNPs on a reference genome.
.TP
scanreads
Obtain error profiles form mapped reads for simulation.
.TP
simreads
Simulates long reads (Pacio or ONT).
.TP
eval
Evaluates a VCF file after SV calling over simulated data.
.PP
\fB\-\-\fR Comparison/filtering
.TP
merge
Compare or merge VCF files to generate a consensus or multi sample VCF files.
.IP
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).
.PP
\fB\-\-\fR Conversion
.TP
bincov
Bins coverage vector to a bed file to filter SVs in low MQ regions
.TP
vcftobed
Converts a VCF file to a bed file
.TP
bedtovcf
Converts a bed file to a VCF file
.TP
smaptovcf
Converts the smap file to a VCF file (beta version)
.TP
bedpetovcf
Converts a bedpe file to a VCF file (beta version)
.TP
hapcuttovcf
Converts the Hapcut2 final file to a VCF file using the original SNP file provided to Hapcut2
.TP
convertAssemblytics
Converts Assemblytics to a VCF file
.SH AUTHOR
 This manpage was written by Nilesh Patra for the Debian distribution and
 can be used for any other usage of the program.