modules/bcftools_merge

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

List containing 2 or more vcf files
e.g. [ ‘file1.vcf’, ‘file2.vcf’ ]

List containing the tbi index files corresponding to the vcfs input files
e.g. [ ‘file1.vcf.tbi’, ‘file2.vcf.tbi’ ]

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

(Optional) The fasta reference file (only necessary for the --gvcf FILE parameter)

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

(Optional) The fasta reference file index (only necessary for the --gvcf FILE parameter)

Groovy Map containing bed information
e.g. [ id:‘genome’ ]

(Optional) The bed regions to merge on