Description

Obtains per-sample observations for the actual calling process with varlociraptor calls

Input

name:type
description
pattern

meta

:map

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

bam

:file

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

bai

:file

Index of the BAM/CRAM/SAM file

*.{bai,crai,sai}

candidates

:file

Sorted BCF/VCF file

*.{bcf,vcf,vcf.gz}

alignment_json

:file

File containing alignment properties obtained with varlociraptor/estimatealignmentproperties

*.json

fasta

:file

Reference fasta file

*.{fasta}

fai

:file

Index for reference fasta file (must be with samtools index)

*.{fai}

Output

name:type
description
pattern

bcf

meta

:map

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

*.bcf

:file

BCF file containing sample observations

*.bcf

versions_varlociraptor

${task.process}

:string

The process the versions were collected from

varlociraptor

:string

The tool name

varlociraptor --version | sed 's/^varlociraptor //'

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The process the versions were collected from

varlociraptor

:string

The tool name

varlociraptor --version | sed 's/^varlociraptor //'

:string

The command used to generate the version of the tool

Tools

varlociraptor
GPL v3

Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.

varlociraptor.github.io/docs/estimating varlociraptor.github.io/docs/calling https://github.com/varlociraptor/varlociraptor 10.1186/s13059-020-01993-6
included in
sarek
maintainers
Github user FriederikeHanssen
Github user famosab
get in touch
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