Description

Apply base quality score recalibration (BQSR) to a bam file

Input

Name
Description
Pattern

meta (map)

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

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
Description
Pattern

meta (map)

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

versions (file)

File containing software versions

versions.yml

bam (file)

Recalibrated BAM file

*.{bam}

cram (file)

Recalibrated CRAM file

*.{cram}

Tools

gatk4 Documentation

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.

doi: 10.1158/1538-7445.AM2017-3590License: Apache-2.0
Authors