Description

Determines the baseline contig ploidy for germline samples given counts data

Input

name:type
description
pattern

meta{:bash}

:map

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

counts{:bash}

:file

One or more count TSV files created with gatk/collectreadcounts

*.tsv

bed{:bash}

:file

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

*.bed

exclude_beds{:bash}

:file

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

*.bed

meta2{:bash}

:map

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

ploidy_model{:bash}

:directory

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

contig_ploidy_table{:bash}

:file

The contig ploidy priors table

*.tsv

Output

name:type
description
pattern

calls{:bash}

meta{:bash}

:map

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

${prefix}-calls{:bash}

:directory

A folder containing the calls from the input files

*-calls/

model{:bash}

meta{:bash}

:map

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

${prefix}-model{:bash}

: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/

versions_gatk4{:bash}

${task.process}{:bash}

:string

The name of the process

gatk4{:bash}

:string

The name of the tool

gatk --version | sed -n '/GATK.*v/s/.*v//p'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

gatk4{:bash}

:string

The name of the tool

gatk --version | sed -n '/GATK.*v/s/.*v//p'{:bash}

:eval

The expression to obtain the version of the tool

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
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maintainer
Github user nvnieuwk
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