Description

Annotation and Ranking of Structural Variation

Input

name:type
description
pattern

meta:map

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

]

sv_vcf:file

A VCF or BED file containing the structural variants to be annotated

*.{bed,vcf,vcf.gz}

sv_vcf_index:file

OPTIONAL - The index for gzipped VCF files

*.tbi

candidate_small_variants:file

OPTIONAL - A file containing candidate small variants

*.{vcf,vcf.gz}

meta2:map

Groovy Map containing annotations information

annotations:directory

The directory containing the annotations (URL to download this will be made available soon) For now this can be downloaded in the way defined in the repo (https://github.com/lgmgeo/AnnotSV#quick-installation)

meta3:map

Groovy Map containing candidate genes information

candidate_genes:file

OPTIONAL - A file containing genes (either space-separated, tab-separated or line-break-separated)

*.txt

meta4:map

Groovy Map containing candidate false positive SNV information

false_positive_snv:file

OPTIONAL - A VCF file containing small variant candidates

*.{vcf,vcf.gz}

meta5:map

Groovy Map containing candidate gene transcripts information

gene_transcripts:file

OPTIONAL - A file containing the preferred gene transcripts to be used in priority during annotation (either space-separated or tab-separated)

*.txt

Output

name:type
description
pattern

tsv

meta:map

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

]

*.tsv:file

A TSV file containing the annotated variants

*.tsv

unannotated_tsv

meta:map

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

]

*.unannotated.tsv:file

OPTIONAL - TSV file containing the unannotated variants

*.unannotated.tsv

vcf

meta:map

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

]

*.vcf:file

OPTIONAL - A VCF file containing the annotated variants (created when -vcf 1 is specified in the args)

*.vcf

versions

versions.yml:file

File containing software versions

versions.yml

Tools

annotsv
GPL-3.0

Annotation and Ranking of Structural Variation