Description

Annotates intervals with GC content, mappability, and segmental-duplication content

Input

name:type
description
pattern

meta{:bash}

:map

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

intervals{:bash}

:file

One or more interval files to annotate

*.{interval_list,list,bed}

meta2{:bash}

:map

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

fasta{:bash}

:file

The reference FASTA file

*.{fasta,fa}

meta3{:bash}

:map

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

fasta_fai{:bash}

:file

The index of the reference FASTA file

*.fai

meta4{:bash}

:map

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

dict{:bash}

:file

The sequence dictionary reference FASTA file

*.dict

meta5{:bash}

:map

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

mappable_regions{:bash}

:file

Optional - Umap single-read mappability track The track should correspond to the appropriate read length and overlapping intervals must be merged

*.bed(.gz)?

meta6{:bash}

:map

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

mappable_regions_tbi{:bash}

:file

Optional - The index of the gzipped umap single-read mappability track

*.bed.gz.tbi

meta7{:bash}

:map

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

segmental_duplication_regions{:bash}

:file

Optional - Segmental-duplication track

*.bed(.gz)?

meta8{:bash}

:map

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

segmental_duplication_regions_tbi{:bash}

:file

Optional - The index of the gzipped segmental-duplication track

*.bed.gz.tbi

Output

name:type
description
pattern

annotated_intervals{:bash}

meta{:bash}

:map

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

*.tsv{:bash}

:file

The output TSV file with a SAM-style header containing the annotated intervals

*.tsv

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

gatk4
Apache-2.0

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/categories/360002369672s 10.1158/1538-7445.AM2017-3590
included in
createpanelrefs
maintainer
Github user nvnieuwk
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