Description

Generate recalibration table for Base Quality Score Recalibration (BQSR)

Input

name:type
description
pattern

meta{:bash}

:map

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

input{:bash}

:file

BAM/CRAM file from alignment

*.{bam,cram}

input_index{:bash}

:file

BAI/CRAI file from alignment

*.{bai,crai}

intervals{:bash}

:file

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

fasta{:bash}

:file

The reference fasta file

*.fasta

fai{:bash}

:file

Index of reference fasta file

*.fasta.fai

dict{:bash}

:file

GATK sequence dictionary

*.dict

known_sites{:bash}

:file

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

*.vcf.gz

known_sites_tbi{:bash}

:file

Tabix index of the known_sites (optional)

*.vcf.gz.tbi

Output

name:type
description
pattern

table{:bash}

meta{:bash}

:map

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

*.table{:bash}

:file

Recalibration table from BaseRecalibrator

*.{table}

versions{:bash}

versions.yml{:bash}

: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