Add or remove annotations.
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input
:file
Query VCF or BCF file, can be either uncompressed or compressed
index
Index of the query VCF or BCF file
annotations
Bgzip-compressed file with annotations
annotations_index
Index of the annotations file
columns
List of columns in the annotations file, one name per row
header_lines
Contains lines to append to the output VCF header
rename_chrs
Rename annotations according to this file containing “old_name new_name\n” pairs separated by whitespaces, each on a separate line.
vcf
${prefix}.${extension}
Compressed annotated VCF file
*{vcf,vcf.gz,bcf,bcf.gz}
tbi
${prefix}.${extension}.tbi
Alternative VCF file index
*.tbi
csi
${prefix}.${extension}.csi
Default VCF file index
*.csi
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
