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:false ]

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

vcf

meta:map

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

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

VCF normalized output file

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

tbi

meta:map

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

*.tbi:file

Alternative VCF file index

*.tbi

csi

meta:map

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

*.csi:file

Default VCF file index

*.csi

versions

versions.yml: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

http://samtools.github.io/bcftools/bcftools http://www.htslib.org/doc/bcftools 10.1093/bioinformatics/btp352
mag phaseimpute radseq raredisease tbanalyzer variantbenchmarking
Github user abhi18av
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