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

]

input:file

BAM/CRAM file from alignment

*.{bam,cram}

input_index:file

BAI/CRAI file from alignment

*.{bai,crai}

bqsr_table:file

Recalibration table from gatk4_baserecalibrator

intervals:file

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

fasta:file

The reference fasta file

*.fasta

fai:file

Index of reference fasta file

*.fasta.fai

dict:file

GATK sequence dictionary

*.dict

Output

name:type
description
pattern

bam

meta:map

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

]

*.bam:file

Recalibrated BAM file

*.{bam}

cram

meta:map

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

]

*.cram:file

Recalibrated 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.

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/categories/360002369672s 10.1158/1538-7445.AM2017-3590
included in
sarek
maintainers
Github user yocra3
Github user FriederikeHanssen
Github user maxulysse
get in touch
Ask a question on Slack Open an issue on GitHub