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