Filter a vcf file based on size and/or regions to ignore
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
vcf_file{:bash}
:file
VCF file to filter
bed{:bash}
BED file with regions to ignore (NA to disable)
minsv{:bash}
:integer
Min SV size (-1 to disable)
maxsv{:bash}
Max SV size (-1 to disable)
minallelefreq{:bash}
:float
Min allele frequency (0-1)
minnumreads{:bash}
Min number of reads support [RE flag (-1 to disable)]
vcf{:bash}
*.vcf{:bash}
Filtered VCF file
*.{vcf}
versions_survivor{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
survivor{:bash}
The name of the tool
SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
Toolset for SV simulation, comparison and filtering
