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 )
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
git clone https://github.com/fritzsedlazeck/SURVIVOR.git cd SURVIVOR/Debug make
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```
If you have questions or encounter a problem please contact: email@example.com