Description

This command replaces the former bcftools view caller. Some of the original functionality has been temporarily lost in the process of transition under htslib, but will be added back on popular demand. The original calling model can be invoked with the -c option.

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.gz}

csi (file)

Default VCF file index

*.csi

tbi (file)

Alternative VCF file index

*.tbi

versions (file)

File containing software versions

versions.yml

Tools

view
MIT

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