Description

Merge unmapped with mapped BAM files

Input

name:type
description
pattern

meta

:map

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

aligned

:file

The aligned bam file

*.{bam}

unmapped

:file

The unmapped bam file

*.{bam}

meta2

:map

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

fasta

:file

The reference fasta file

meta3

:map

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

dict

:file

GATK sequence dictionary

Output

name:type
description
pattern

bam

meta

:file

The merged bam file

*.bam

*.bam

:file

The merged bam file

*.bam

versions_gatk4

${task.process}

:string

The name of the process

gatk4

:string

The name of the tool

gatk --version | sed -n '/GATK.*v/s/.*v//p'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

gatk4

:string

The name of the tool

gatk --version | sed -n '/GATK.*v/s/.*v//p'

: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
included in
raredisease
maintainers
Github user kevinmenden
Github user ramprasadn
get in touch
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