Description

CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome.

Input

name:type
description
pattern

meta{:bash}

:map

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

vcf{:bash}

:file

Input file for annotation in vcf or vcf.gz format

*.{vcf,vcf.gz}

meta2{:bash}

:map

Groovy Map containing reference information e.g. [ id:‘test’ ]

annotation_dir{:bash}

:directory

Path to folder containing the vcf files with precomputed CADD scores. This folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation.

meta3{:bash}

:map

Groovy Map containing reference information e.g. [ id:‘test’ ]

prescored_dir{:bash}

:directory

Path to folder containing prescored CADD score files. Expected structure mirrors data/prescored/ from the CADD-scripts installation: <prescored_dir>/ GRCh38_v1.7/ incl_anno/ # *.tsv.gz + *.tsv.gz.tbi (scores with annotations) no_anno/ # *.tsv.gz + *.tsv.gz.tbi (scores only) GRCh37_v1.7/ incl_anno/ no_anno/ See https://github.com/kircherlab/CADD-scripts/#manual-installation for details.

Output

name:type
description
pattern

tsv{:bash}

meta{:bash}

:map

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

${prefix}.tsv.gz{:bash}

:file

Annotated tsv file

*.{tsv,tsv.gz}

versions_cadd{:bash}

${task.process}{:bash}

:string

The name of the process

cadd{:bash}

:string

The name of the tool

1.7.3{:bash}

:string

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

cadd{:bash}

:string

The name of the tool

1.7.3{:bash}

:string

The expression to obtain the version of the tool

Tools

included in
raredisease
maintainer
Github user ramprasadn
get in touch
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