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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

tsv (file)

A TSV file containing the annotated variants

*.tsv

unannotated_tsv (file)

OPTIONAL - TSV file containing the unannotated variants

*.unannotated.tsv

vcf (file)

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

*.vcf
maintainer
Github user nvnieuwk
get in touch
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Tools

annotsv
GPL-3.0

Annotation and Ranking of Structural Variation

lbgi.fr/AnnotSV https://github.com/lgmgeo/AnnotSV 10.1093/bioinformatics/bty304