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

Fasta file

*.{fasta}

fasta_fai:file

Fasta index file

*.{fai}

Output

name:type
description
pattern

cram

meta:map

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

]

*cram:file

Marked duplicates CRAM file

*.{cram}

bam

meta:map

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

]

*bam:file

Marked duplicates BAM file

*.{bam}

crai

meta:map

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

]

*.crai:file

CRAM index file

*.{cram.crai}

bai

meta:map

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

]

*.bai:file

BAM index file

*.{bam.bai}

metrics

meta:map

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

]

*.metrics:file

Duplicate metrics file generated by GATK

*.{metrics.txt}

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.