normalizes variants in a VCF file
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
[ id:'test', single_end:false ]
vcf{:bash}
:file
The VCF file to normalize
*.vcf(.gz)?
tbi{:bash}
The tabix index of the VCF file when bgzipped
*.tbi
intervals{:bash}
The intervals of the variants of normalize
*.bed
meta2{:bash}
Groovy Map containing reference information e.g. [ id:'test', single_end:false ]
fasta{:bash}
The reference fasta file
*.{fasta,fn,fna,fa}
meta3{:bash}
Groovy Map containing reference index information e.g. [ id:'test', single_end:false ]
fai{:bash}
The index of the reference fasta file (OPTIONAL)
*.fai
*.vcf.gz{:bash}
The normalized VCF file
*.vcf.gz
${fasta}.fai{:bash}
The created index of the reference fasta file (only when the fai wasn’t supplied)
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
A tool set for short variant discovery in genetic sequence data
