modules/gatk4_baserecalibratorspark

Generate recalibration table for Base Quality Score Recalibration (BQSR)

base quality score recalibrationtablebqsrgatk4sortspark

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

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

`meta` (map)

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

]

`versions` (file)

File containing software versions

versions.yml

`table` (file)

Recalibration table from BaseRecalibrator

*.{table}

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_baserecalibratorspark

Description

Input

`meta` (map)

`input` (file)

`input_index` (file)

`intervals` (file)

`fasta` (file)

`fai` (file)

`dict` (file)

`known_sites` (file)

`known_sites_tbi` (file)

Output

`meta` (map)

`versions` (file)

`table` (file)

included in

maintainers

get in touch

Tools

gatk4
Apache-2.0

modules/gatk4_baserecalibratorspark

Description

Input

meta (map)

input (file)

input_index (file)

intervals (file)

fasta (file)

fai (file)

dict (file)

known_sites (file)

known_sites_tbi (file)

Output

meta (map)

versions (file)

table (file)

included in

maintainers

get in touch

Tools

gatk4 Apache-2.0

`meta` (map)

`input` (file)

`input_index` (file)

`intervals` (file)

`fasta` (file)

`fai` (file)

`dict` (file)

`known_sites` (file)

`known_sites_tbi` (file)

`meta` (map)

`versions` (file)

`table` (file)

gatk4
Apache-2.0