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

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 (file)

File containing software versions

versions.yml
maintainer
Github user FriederikeHanssen
get in touch
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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