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

]

bam (file)

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

candidates (file)

Sorted BCF/VCF file

*.{bcf,vcf,vcf.gz}

alignment_json (file)

File containing alignment properties obtained with varlociraptor/estimatealignmentproperties

*.json

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

]

versions (file)

File containing software versions

versions.yml

vcf_gz (file)

Compressed VCF file containing sample observations

*.vcf.gz

bcf_gz (file)

BCF file containing sample observations

*.bcf.gz

vcf (file)

VCF file containing sample observations

*.vcf

bcf (file)

BCF file containing sample observations

*.bcf
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 varlociraptor.github.io/docs/calling https://github.com/varlociraptor/varlociraptor 10.1186/s13059-020-01993-6