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:map

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

]

bam:file

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

meta2:map

Groovy Map containing reference information e.g. [ id:‘test’, single_end

]

fasta:file

Reference fasta file

*.{fasta}

meta3:map

Groovy Map containing reference index information e.g. [ id:‘test’, single_end

]

fai:file

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

*.{fai}

Output

name:type
description
pattern

alignment_properties_json

meta:map

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

]

*.alignment-properties.json:file

File containing alignment properties

*.alignment-properties.json

versions

versions.yml:file

File containing software versions

versions.yml

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
maintainer
Github user FriederikeHanssen
get in touch
Ask a question on Slack Open an issue on GitHub