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}

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

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

bcf_gz

meta:map

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

]

*.bcf.gz:file

BCF file containing sample observations

*.bcf.gz

vcf_gz

meta:map

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

]

*.vcf.gz:file

Compressed VCF file containing sample observations

*.vcf.gz

bcf

meta:map

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

]

*.bcf:file

BCF file containing sample observations

*.bcf

vcf

meta:map

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

]

*.vcf:file

VCF file containing sample observations

*.vcf

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 varlociraptor.github.io/docs/calling https://github.com/varlociraptor/varlociraptor 10.1186/s13059-020-01993-6
maintainer
Github user FriederikeHanssen
get in touch
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