Description

In order to judge about candidate indel and structural variants, Varlociraptor needs to know about certain properties of the underlying sequencing experiment in combination with the used read aligner.

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

bai{:bash}

:file

Index of sorted BAM/CRAM/SAM file

*.{bai,crai,sai}

fasta{:bash}

:file

Reference fasta file

*.{fasta}

fai{:bash}

:file

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

*.{fai}

Output

name:type
description
pattern

alignment_properties_json{:bash}

meta{:bash}

:map

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

*.alignment-properties.json{:bash}

:file

File containing alignment properties

*.alignment-properties.json

versions_varlociraptor{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

varlociraptor{:bash}

:string

The tool name

varlociraptor --version | sed 's/^varlociraptor //'{:bash}

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

varlociraptor{:bash}

:string

The tool name

varlociraptor --version | sed 's/^varlociraptor //'{:bash}

: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 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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