Description

Compresses VCF files

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

vcf (file)

VCF file

*.{vcf}

tbi (file)

tabix index file

*.{tbi}

fasta (file)

FASTA reference file

*.{fasta,fa}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

fasta (file)

FASTA reference consensus file

*.{fasta,fa}

versions (file)

File containing software versions

versions.yml
included in
magviralrecon
authors
Github user joseespinosa Github user drpatelh
get in touch
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Tools

consensus
MIT

Create consensus sequence by applying VCF variants to a reference fasta file.

http://samtools.github.io/bcftools/bcftools http://www.htslib.org/doc/bcftools10.1093/bioinformatics/btp352