SURVIVOR1
<short_description>
Usage
SURVIVOR <command>
[options]
Overview
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
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).