Description

Creates an interval list from a bed file and a reference dict

Input

name:type
description
pattern

meta:map

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

bed:file

Input bed file

*.bed

meta2:map

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

dict:file

Sequence dictionary

*.dict

Output

name:type
description
pattern

interval_list

meta:file

gatk interval list file

*.interval_list

*.interval_list:file

gatk interval list file

*.interval_list

_list:file

gatk interval list file

*.interval_list

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
createpanelrefs raredisease rnadnavar rnafusion rnavar
Github user kevinmenden
Github user ramprasadn
Ask a question on Slack Open an issue on GitHub