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: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 ]

*.gz:file

VCF normalized output file

*.{vcf.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
Github user abhi18av
Github user LouisLeNezet
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