Description

Adds predicted functional consequence, gene overlap, and noncoding element overlap annotations to SV VCF from GATK-SV pipeline. Input files are an SV VCF, a GTF file containing primary or canonical transcripts, and a BED file containing noncoding elements. Output file is an annotated SV VCF.

Input

name:type
description
pattern

meta{:bash}

:map

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

vcf{:bash}

:file

A VCF file created with a structural variant caller

*.vcf.gz

tbi{:bash}

:file

The index file of the VCF

*.vcf.gz.tbi

bed{:bash}

:file

Regions to limit the analysis to

*.bed

non_coding_bed{:bash}

:file

File containing noncoding regions

*.bed

meta2{:bash}

:map

Groovy Map containing FASTA information e.g. [ id:‘test’, single_end:false ]

fasta{:bash}

:file

Optional - reference FASTA file needed when the input is a CRAM file

*.{fasta,fa}

meta3{:bash}

:map

Groovy Map containing FAI information e.g. [ id:‘test’, single_end:false ]

fasta_fai{:bash}

:file

Optional - index of the reference FASTA file needed when the input is a CRAM file

*.fai

meta4{:bash}

:map

Groovy Map containing DICT information e.g. [ id:‘test’, single_end:false ]

dict{:bash}

:file

Optional - sequence dictionary of the reference FASTA file needed when the input is a CRAM file

*.dict

meta5{:bash}

:map

Groovy Map containing GTF information e.g. [ id:‘test’, single_end:false ]

gtf{:bash}

:file

Optional - GTF file containing transcript information

*.gtf

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

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

*.vcf.gz{:bash}

:file

The annotated structural variant VCF

*.vcf.gz

tbi{:bash}

meta{:bash}

:map

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

*.vcf.gz.tbi{:bash}

:file

The index of the VCF

*.vcf.gz.tbi

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

maintainer
Github user nvnieuwk
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