Description

Filters intervals based on annotations and/or count statistics.

Input

name:type
description
pattern

meta{:bash}

:map

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

intervals{:bash}

:file

Processed interval list file (processed_intervals.interval_list)

*.interval_list

meta2{:bash}

:map

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

read_counts{:bash}

:file

Read counts input file

*.{tsv, hdf5}

meta3{:bash}

:map

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

annotated_intervals{:bash}

:file

Annotated intervals TSV file (annotated_intervals.tsv).

*.tsv

Output

name:type
description
pattern

interval_list{:bash}

meta{:bash}

:map

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

*.interval_list{:bash}

:file

Filtered interval list file

*.interval_list

versions_gatk4{:bash}

${task.process}{:bash}

:string

The name of the process

gatk4{:bash}

:string

The name of the tool

gatk --version | sed -n '/GATK.*v/s/.*v//p'{:bash}

:eval

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

gatk4{:bash}

:string

The name of the tool

gatk --version | sed -n '/GATK.*v/s/.*v//p'{:bash}

:eval

The expression to obtain the version of the tool

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
maintainers
Github user ryanjameskennedy
Github user ViktorHy
get in touch
Ask a question on Slack Open an issue on GitHub