Description

Prepares bins for coverage collection.

Input

Name (Type)
Description
Pattern

meta (map)

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

fasta (file)

The reference fasta file

*.fasta

meta2 (map)

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

fai (file)

Index of reference fasta file

*.fasta.fai

meta3 (map)

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

dict (file)

GATK sequence dictionary

*.dict

meta4 (map)

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

intervals (file)

Interval file (bed or interval_list) with the genomic regions to be included from the analysis (optional)

*.{bed,interval_list}

meta5 (map)

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

exclude_intervals (file)

Interval file (bed or interval_list) with the genomic regions to be excluded from the analysis (optional)

*.{bed,interval_list}

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions

versions.yml

interval_list (file)

Processed interval list file

*.{bed,interval_list}
included in
createpanelrefs raredisease
maintainers
Github user ryanjameskennedy
Github user ViktorHy
Github user ramprasadn
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