Merge VCF files
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
vcfs
:file
List containing 2 or more vcf files e.g. [ ‘file1.vcf’, ‘file2.vcf’ ]
tbis
List containing the tbi index files corresponding to the vcfs input files e.g. [ ‘file1.vcf.tbi’, ‘file2.vcf.tbi’ ]
bed
(Optional) The bed regions to merge on
*.bed
meta2
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta
(Optional) The fasta reference file (only necessary for the --gvcf FILE parameter)
--gvcf FILE
*.{fasta,fa}
fai
(Optional) The fasta reference file index (only necessary for the --gvcf FILE parameter)
*.fai
vcf
*.{bcf,vcf}{,.gz}
merged output file
*.{vcf,vcf.gz,bcf,bcf.gz}
index
*.{csi,tbi}
index of merged output
versions_bcftools
${task.process}
:string
The process the versions were collected from
bcftools
The tool name
bcftools --version | sed '1!d; s/^.*bcftools //'
The command used to generate the version of the tool
versions
Merge VCF files.
