Description

Generate recalibration table for Base Quality Score Recalibration (BQSR)

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}

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

known_sites:file

VCF files with known sites for indels / snps (optional)

*.vcf.gz

known_sites_tbi:file

Tabix index of the known_sites (optional)

*.vcf.gz.tbi

Output

name:type
description
pattern

table

meta:map

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

]

*.table:file

Recalibration table from BaseRecalibrator

*.{table}

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