Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

]

intervals (file)

One or more interval files to annotate

*.{interval_list,list,bed}

meta2 (map)

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

fasta (file)

The reference FASTA file

*.{fasta,fa}

meta3 (map)

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

fasta_fai (file)

The index of the reference FASTA file

*.fai

meta4 (map)

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

dict (file)

The sequence dictionary reference FASTA file

*.dict

meta5 (map)

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

mappable_regions (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 (map)

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

mappable_regions_tbi (file)

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

*.bed.gz.tbi

meta7 (map)

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

segmental_duplication_regions (file)

Optional - Segmental-duplication track

*.bed(.gz)?

meta8 (map)

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

segmental_duplication_regions_tbi (file)

Optional - The index of the gzipped segmental-duplication track

*.bed.gz.tbi

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

annotated_intervals (file)

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

*.tsv
included in
createpanelrefs
maintainer
Github user nvnieuwk
get in touch
Ask a question on Slack Open an issue on GitHub

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