fritzsedlazeck / Survivor
Licence: mit
Toolset for SV simulation, comparison and filtering
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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: [email protected]
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