Merge VCF files
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
vcfs{:bash}
:file
List containing 2 or more vcf files e.g. [ ‘file1.vcf’, ‘file2.vcf’ ]
tbis{:bash}
List containing the tbi index files corresponding to the vcfs input files e.g. [ ‘file1.vcf.tbi’, ‘file2.vcf.tbi’ ]
meta2{:bash}
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta{:bash}
(Optional) The fasta reference file (only necessary for the --gvcf FILE parameter)
--gvcf FILE
*.{fasta,fa}
meta3{:bash}
fai{:bash}
(Optional) The fasta reference file index (only necessary for the --gvcf FILE parameter)
*.fai
meta4{:bash}
Groovy Map containing bed information e.g. [ id:‘genome’ ]
bed{:bash}
(Optional) The bed regions to merge on
*.bed
vcf{:bash}
*.{bcf,vcf}{,.gz}{:bash}
merged output file
*.{vcf,vcf.gz,bcf,bcf.gz}
index{:bash}
*.{csi,tbi}{:bash}
index of merged output
*.{csi,tbi}
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Merge VCF files.
