Description

View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

vcf (file)

The vcf file to be inspected.
e.g. ‘file.vcf’

index (file)

The tab index for the VCF file to be inspected.
e.g. ‘file.tbi’

regions (file)

Optionally, restrict the operation to regions listed in this file.
e.g. ‘file.vcf’

targets (file)

Optionally, restrict the operation to regions listed in this file (doesn’t rely upon index files)
e.g. ‘file.vcf’

samples (file)

Optional, file of sample names to be included or excluded.
e.g. ‘file.tsv’

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

vcf (file)

VCF normalized output file

*.{vcf,vcf.gz,bcf,bcf.gz}

csi (file)

Default VCF file index

*.csi

tbi (file)

Alternative VCF file index

*.tbi

versions (file)

File containing software versions

versions.yml
included in
mag phaseimpute raredisease variantbenchmarking
maintainer
Github user abhi18av
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Tools

view
MIT

View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF

http://samtools.github.io/bcftools/bcftools http://www.htslib.org/doc/bcftools 10.1093/bioinformatics/btp352