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:file
Optional index file for the VCF
*.{tbi,csi}
regions_file:file
Optional. Restrict to regions listed in a file
*.{bed,bed.gz,txt,tsv}
meta2:map
Groovy Map containing pedigree information
pedigree:file
Optional pedigree for jvarkit
*.{ped,pedigree}
output
Groovy Map containing VCF information e.g. [ id:‘test’, single_end:false ]
*.${extension}:file
Output file
*.{txt,html}
versions
versions.yml:file
File containing software versions
versions.yml
Java utilities for Bioinformatics.
$args2
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
$args1
