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