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