Add or remove annotations.
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input{:bash}
:file
Query VCF or BCF file, can be either uncompressed or compressed
index{:bash}
Index of the query VCF or BCF file
annotations{:bash}
Bgzip-compressed file with annotations
annotations_index{:bash}
Index of the annotations file
columns{:bash}
List of columns in the annotations file, one name per row
header_lines{:bash}
Contains lines to append to the output VCF header
rename_chrs{:bash}
Rename annotations according to this file containing “old_name new_name\n” pairs separated by whitespaces, each on a separate line.
vcf{:bash}
${prefix}.${extension}{:bash}
Compressed annotated VCF file
*{vcf,vcf.gz,bcf,bcf.gz}
tbi{:bash}
${prefix}.${extension}.tbi{:bash}
Alternative VCF file index
*.tbi
csi{:bash}
${prefix}.${extension}.csi{:bash}
Default VCF file index
*.csi
versions_bcftools{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
bcftools{:bash}
The tool name
bcftools --version | sed '1!d; s/^.*bcftools //'{:bash}
The command used to generate the version of the tool
versions{:bash}
