Description

Sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that.

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’

target_gt

:string

Genotypes to change

new_gt

:string

Genotypes to set

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’

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 output file containing set genotypes

*.{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

bcftools
MIT

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.

args_id: $args
samtools.github.io/bcftools/howtos samtools.github.io/bcftools/bcftools https://github.com/samtools/bcftools 10.1093/bioinformatics/btp352

bcftools plugin setGT
MIT

Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The setGT plugin sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that.

args_id: $args2
samtools.github.io/bcftools/howtos/plugins samtools.github.io/bcftools/howtos/plugin.setGT https://github.com/samtools/bcftools 10.1093/bioinformatics/btp352
maintainer
Github user eweizy
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