modules/gatk4_mergebamalignment

Merge unmapped with mapped BAM files

alignmentbamgatk4mergemergebamalignment

https://github.com/nf-core/modules/[...]/modules/nf-core/gatk4/mergebamalignment

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

modules/gatk4_mergebamalignment

Description

Input

meta:map

aligned:file

unmapped:file

meta2:map

fasta:file

meta3:map

dict:file