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

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
included in
raredisease
maintainers
Github user kevinmenden
Github user ramprasadn
get in touch
Ask a question on Slack Open an issue on GitHub