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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

bam (file)

Recalibrated BAM file

*.{bam}

cram (file)

Recalibrated CRAM file

*.{cram}
included in
rnadnavar rnavar sarek
maintainers
Github user yocra3
Github user FriederikeHanssen
get in touch
Ask a question on Slack Open an issue on GitHub

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