modules/gatk4_markduplicates

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.

bamgatk4markduplicatessort

https://github.com/nf-core/modules/[...]/modules/nf-core/gatk4/markduplicates

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:false ]

`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:false ]

`*cram`
`:file`

Marked duplicates CRAM file

*.{cram}

`bam`

`meta`
`:map`

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

`*bam`
`:file`

Marked duplicates BAM file

*.{bam}

`crai`

`meta`
`:map`

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

`*.crai`
`:file`

CRAM index file

*.{cram.crai}

`bai`

`meta`
`:map`

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

`*.bai`
`:file`

BAM index file

*.{bam.bai}

`metrics`

`meta`
`:map`

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

`*.metrics`
`:file`

Duplicate metrics file generated by GATK

*.{metrics.txt}

`versions_gatk4`

`${task.process}`
`:string`

The name of the process

`gatk4`
`:string`

The name of the tool

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

The expression to obtain the version of the tool

`versions_samtools`

`${task.process}`
`:string`

The name of the process

`samtools`
`:string`

The name of the tool

`samtools version | sed '1!d;s/.* //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`gatk4`
`:string`

The name of the tool

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`samtools`
`:string`

The name of the tool

`samtools version | sed '1!d;s/.* //'`
`:eval`

The expression to obtain the version of the tool

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.

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard- https://github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590

modules/gatk4_markduplicates

Description

Input

meta :map

bam :file

fasta :file

fasta_fai :file

Output

cram

meta :map

*cram :file

bam

meta :map

*bam :file

crai

meta :map

*.crai :file

bai

meta :map

*.bai :file

metrics

meta :map

*.metrics :file

versions_gatk4

${task.process} :string

gatk4 :string

gatk --version | sed -n '/GATK.*v/s/.*v//p' :eval

versions_samtools

${task.process} :string

samtools :string

samtools version | sed '1!d;s/.* //' :eval

Topics

versions

${task.process} :string

gatk4 :string

gatk --version | sed -n '/GATK.*v/s/.*v//p' :eval

${task.process} :string

samtools :string

samtools version | sed '1!d;s/.* //' :eval

Tools

gatk4MIT

included in

maintainers

get in touch

`meta`
`:map`

`bam`
`:file`

`fasta`
`:file`

`fasta_fai`
`:file`

`cram`

`meta`
`:map`

`*cram`
`:file`

`bam`

`meta`
`:map`

`*bam`
`:file`

`crai`

`meta`
`:map`

`*.crai`
`:file`

`bai`

`meta`
`:map`

`*.bai`
`:file`

`metrics`

`meta`
`:map`

`*.metrics`
`:file`

`versions_gatk4`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

`versions_samtools`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:eval`

`versions`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:eval`

gatk4
MIT