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