Description

Filters intervals based on annotations and/or count statistics.

Input

Name (Type)
Description
Pattern

meta (map)

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

intervals (file)

Processed interval list file (processed_intervals.interval_list)

*.interval_list

meta2 (map)

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

]

read_counts (file)

Read counts input file

*.{tsv, hdf5}

meta3 (map)

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

]

annotated_intervals (file)

Annotated intervals TSV file (annotated_intervals.tsv).

*.tsv

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

interval_list (file)

Filtered interval list file

*.interval_list
included in
createpanelrefs
maintainers
Github user ryanjameskennedy
Github user ViktorHy
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