Description

Assigns all the reads in a file to a single new read-group

Input

Name (Type)
Description
Pattern

meta (map)

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

]

meta2 (map)

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

]

meta3 (map)

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

]

bam (file)

Input BAM file

*.{bam}

fasta (file)

Reference genome file

*.{fasta,fa,fasta.gz,fa.gz}

fasta_index (file)

Reference genome index file

*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

bam (file)

Output BAM file

*.{bam}

bai (file)

An optional BAM index file

*.{bai}

cram (file)

Output CRAM file

*.{cram}
maintainers
Github user sateeshperi
Github user mjcipriano
Github user hseabolt
Github user cmatKhan
Github user muffato
get in touch
Ask a question on Slack Open an issue on GitHub

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