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:false ]

read_counts:file

Read counts input file

*.{tsv, hdf5}

meta3:map

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

annotated_intervals:file

Annotated intervals TSV file (annotated_intervals.tsv).

*.tsv

Output

name:type
description
pattern

interval_list

meta:map

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

*.interval_list:file

Filtered interval list file

*.interval_list

_list:file

Filtered 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
Github user ryanjameskennedy
Github user ViktorHy
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