modules/gatk4_annotateintervals

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

annotateintervalsannotationbedgatk4intervals

https://github.com/nf-core/modules/[...]/modules/nf-core/gatk4/annotateintervals

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:false ]

`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

`annotated_intervals`

`meta:map`

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

`*.tsv:file`

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

*.tsv

`versions`

`versions.yml: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