Description

This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.

Input

name:type
description
pattern

meta:map

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

]

bam:file

Sorted BAM file

*.{bam}

fasta:file

The reference fasta file

*.fasta

fasta_fai:file

Index of reference fasta file

*.fai

dict:file

GATK sequence dictionary

*.dict

Output

name:type
description
pattern

output

meta:map

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

]

${prefix}:file

Marked duplicates BAM/CRAM file

*.{bam,cram}

bam_index

meta:map

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

]

${prefix}.bai:file

Optional BAM index file

*.bai

metrics

meta:map

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

]

*.metrics:file

Metrics file

*.metrics

versions

versions.yml:file

File containing software versions

versions.yml

Tools

gatk4
MIT

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.