Simulate an SV VCF file based on a reference genome
meta:map
Groovy Map containing fasta information e.g. [ id:'test', single_end:false ]
[ id:'test', single_end:false ]
fasta:file
The reference genome
*.{fasta,fna,fa}
meta2:map
Groovy Map containing fasta index information e.g. [ id:'test', single_end:false ]
fai:file
The index of the reference genome
*.fai
meta3:map
Groovy Map containing parameters information e.g. [ id:'test', single_end:false ]
parameters:file
A text file containing the parameters to be used for the simulation. Gets automatically generated using defaults when this is not supplied
*.txt
snp_mutation_frequency:float
The SNP mutation frequency in the output VCF (0-1)
sim_reads:integer
Whether or not to simulate reads (1==yes, else no)
parameters
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.txt:file
The created parameters file
vcf
*.vcf:file
A VCF containing the simulated variants
*.vcf
bed
*.bed:file
A BED file of the simulated structural variants
*.bed
fasta
*.fasta:file
A Fasta file file containing the variants from the output VCF
*.fasta
insertions
*.insertions.fa:file
A Fasta file file containing insertion sequences
*.insertions.fa
versions
versions.yml:file
File containing software versions
versions.yml
Toolset for SV simulation, comparison and filtering
