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:
Possible options 1: Simulate SV on genome 2: Simulate PacBio reads 3: Evaluate SV calling 4: Merge SV calls (vcf) 5: Merge + Consensus call from different callers/vcf files 6: Extract genes influenced by SVs 7: Filter and convert SV calls from Delly 8: Filter and convert SV calls from Lumpy 9: Filter and convert SV calls from Pindel 10: Convert SV calls from PBHoney (tails) 11: Convert SV calls from Assemblytics 12: Summarize MQ 0 coverage to bed file 13: Summarize SVs events in VCF file
If you have questions or encounter a problem please contact: firstname.lastname@example.org