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}

unaligned (file)

The unmaped 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 (file)

The merged bam file

*.bam

versions (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.