Convert VCF to a user friendly table
meta
:map
Groovy Map containing VCF information e.g. [ id:‘genome’ ]
vcf
:file
Input vcf/bcf file
*.{vcf,bcf,vcf.gz,bcf.gz}
tbi
Optional index file for the VCF
*.{tbi,csi}
regions_file
Optional. Restrict to regions listed in a file
*.{bed,bed.gz,txt,tsv}
meta2
Groovy Map containing pedigree information
pedigree
Optional pedigree for jvarkit
*.{ped,pedigree}
output
Groovy Map containing VCF information e.g. [ id:‘test’, single_end:false ]
*.${extension}
Output file
*.{txt,html}
versions_jvarkit
${task.process}
:string
The name of the process
jvarkit
The name of the tool
jvarkit -v
:eval
The expression to obtain the version of the tool
versions_bcftools
bcftools
bcftools --version |& sed '1!d;s/bcftools //'
versions
Java utilities for Bioinformatics.
$args2
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
$args1
