Description

Determines the baseline contig ploidy for germline samples given counts data

Input

Name (Type)
Description
Pattern

meta (map)

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

]

meta2 (map)

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

counts (file)

One or more count TSV files created with gatk/collectreadcounts

*.tsv

bed (file)

Optional - A bed file containing the intervals to include in the process

*.bed

exclude_beds (file)

Optional - One or more bed files containing intervals to exclude from the process

*.bed

contig_ploidy_table (file)

The contig ploidy priors table

*.tsv

ploidy_model (directory)

Optional - A folder containing the ploidy model.
When a model is supplied to tool will run in CASE mode.
pattern: ‘*.model/’

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

calls (directory)

A folder containing the calls from the input files

*-calls/

model (directory)

A folder containing the model from the input files.
This will only be created in COHORT mode (when no model is supplied to the process).

*-model/
included in
createpanelrefs raredisease
author
Github user nvnieuwk
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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