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
Download SURVIVOR:
git clone https://github.com/fritzsedlazeck/SURVIVOR.git cd SURVIVOR/Debug make
./SURVIVOR ID
to see the individual parameters for each option.
choose the ID from these options:
Possible options
1: Simulate SV on genome
2: Simulate PacBio/ONT reads
3: Evaluate SV calling
4: Convert Bionano smap to vcf file
5: Consensus call from multipe SV calls (vcf files)
6: Extract genes influenced by SVs
7: Filter and convert SV calls from Delly
8: Converts vcf to bedpe
9: Filter and convert SV calls from BED files
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
Please note: SURVIVOR assumes that the sequences in the fasta file for the reference does not exceed 200,000bp per line.
If you have questions or encounter a problem please contact: [email protected]
