Normalize VCF file
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
vcf{:bash}
:file
The vcf file to be normalized e.g. ‘file1.vcf’
*.{vcf,vcf.gz}
tbi{:bash}
An optional index of the VCF file (for when the VCF is compressed)
*.vcf.gz.tbi
meta2{:bash}
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta{:bash}
FASTA reference file
*.{fasta,fa}
*.{vcf,vcf.gz,bcf,bcf.gz}{:bash}
One of uncompressed VCF (.vcf), compressed VCF (.vcf.gz), compressed BCF (.bcf.gz) or uncompressed BCF (.bcf) normalized output file
*.{vcf,vcf.gz,bcf,bcf.gz}
*.tbi{:bash}
Alternative VCF file index
*.tbi
csi{:bash}
*.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}
Normalize VCF files.
