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

]

bam:file

Input BAM file

*.{bam}

meta2:map

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

]

fasta:file

Reference genome file

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

meta3:map

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

]

fasta_index:file

Reference genome index file

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

Output

name:type
description
pattern

bam

meta:map

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

]

*.bam:file

Output BAM file

*.{bam}

bai

meta:map

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

]

*.bai:file

An optional BAM index file

*.{bai}

cram

meta:map

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

]

*.cram:file

Output CRAM file

*.{cram}

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.