SURVIVOR

SURVIVOR is a tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs.

Please see our github wiki for more information (https://github.com/fritzsedlazeck/SURVIVOR/wiki )

Cite:

If you use it in your study please cite:

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast.
Jeffares, Daniel C; Jolly, Clemency; Hoti, Mimoza; Speed, Doug; Shaw, Liam; Rallis, Charalampos; Balloux, Francois; Dessimoz, Christophe; Bähler, Jürg; Sedlazeck, Fritz J.
Nature communications, Vol. 8, 14061, 24.01.2017, p. 1-11. DOI:10.1038/NCOMMS14061

INSTALL:

Download SURVIVOR:

git clone https://github.com/fritzsedlazeck/SURVIVOR.git
cd SURVIVOR/Debug
make

USAGE:

./SURVIVOR ID

to see the individual parameters for each option.

choose the ID from these options:

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```

CONTACT:

If you have questions or encounter a problem please contact: fritz.sedlazeck@gmail.com