modules/gatk4_applybqsr

Apply base quality score recalibration (BQSR) to a bam file

bambase quality score recalibrationbqsrcramgatk4

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

Description

Apply base quality score recalibration (BQSR) to a bam file

Input

name:type

description

pattern

`meta`
`:map`

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

`input`
`:file`

BAM/CRAM file from alignment

*.{bam,cram}

`input_index`
`:file`

BAI/CSI/CRAI file from alignment

*.{bai,csi,crai}

`bqsr_table`
`:file`

Recalibration table from gatk4_baserecalibrator

`intervals`
`:file`

Bed file with the genomic regions included in the library (optional)

`meta2`
`:map`

Groovy Map containing sample information about the reference e.g. [ id:‘genome’ ]

`fasta`
`:file`

The reference fasta file

*.fasta

`fai`
`:file`

Index of reference fasta file

*.fasta.fai

`dict`
`:file`

GATK sequence dictionary

*.dict

`output_format`
`:list`

Output file type and index format as a two-element list. First element: ‘bam’ or ‘cram’. Second element: ‘bai’, ‘csi’, or ‘crai’.

Valid combinations: [‘bam’, ‘bai’], [‘bam’, ‘csi’], [‘cram’, ‘crai’]. Defaults to [‘cram’, ‘crai’] when not provided.

{bam,cram}

Output

name:type

description

pattern

`reads`

`meta`
`:map`

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

`*.{bam,cram}`
`:file`

Recalibrated BAM or CRAM file

*.{bam,cram}

`index`

`meta`
`:map`

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

`*.{bai,csi,crai}`
`:file`

Index of the recalibrated BAM or CRAM file

*.{bai,csi,crai}

`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
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

modules/gatk4_applybqsr

Description

Input

meta :map

input :file

input_index :file

bqsr_table :file

intervals :file

meta2 :map

fasta :file

fai :file

dict :file

output_format :list

Output

reads

meta :map

*.{bam,cram} :file

index

meta :map

*.{bai,csi,crai} :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

gatk4Apache-2.0

included in

maintainers

get in touch

`meta`
`:map`

`input`
`:file`

`input_index`
`:file`

`bqsr_table`
`:file`

`intervals`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`fai`
`:file`

`dict`
`:file`

`output_format`
`:list`

`reads`

`meta`
`:map`

`*.{bam,cram}`
`:file`

`index`

`meta`
`:map`

`*.{bai,csi,crai}`
`: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
Apache-2.0