/BQSR-nf

Nextflow script for base quality score recalibration of bam files using GATK

Primary LanguageNextflowGNU General Public License v3.0GPL-3.0

BQSR-nf

Nextflow pipeline for base quality score recalibration with GATK processing

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Workflow representation

Decription

Nextflow pipeline for base quality score recalibration and quality control of bam files using GATK

Dependencies

  1. Nextflow: for common installation procedures see the IARC-nf repository.

  2. multiQC

  3. GATK4 must be in the PATH variable

  4. GATK bundle VCF files with lists of indels and SNVs (recommended: 1000 genomes indels, dbsnp VCF)

You can provide a config file to customize the multiqc report (see https://multiqc.info/docs/#configuring-multiqc).

Input

Type Description
--input_folder a folder with bam files

Parameters

  • Mandatory

Name Example value Description
--ref ref.fa reference genome fasta file for GATK

  • Optional

Name Default value Description
--cpu 2 number of CPUs
--mem 32 memory for mapping
--output_folder . output folder for aligned BAMs
--snp_vcf dbsnp.vcf VCF file with known variants for GATK BQSR
--indel_vcf Mills_100G_indels.vcf VCF file with known indels for GATK BQSR
--multiqc_config null config yaml file for multiqc

  • Flags

Name Description
--help print usage and optional parameters

Usage

To run the pipeline on a series of bam files in folder bam, a reference genome with indexes at ref.fa, and known snps and indels from the gatk bundle, one can type:

nextflow run iarcbioinfo/BQSR-nf --input_folder bam --ref ref.fa --snp_vcf GATK_bundle/dbsnp_146.hg38.vcf.gz --indel_vcf GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz

Output

Type Description
BAM/file.bam BAM files of alignments or realignments
BAM/file.bam.bai BAI files of alignments or realignments
QC/multiqc_BQSR_report.html multiqc report
QC/multiqc_BQSR_report_data folder with data used to compute multiqc report
QC/BAM/BQSR/file_recal.table table of scores before recalibration
QC/BAM/BQSR/file_post_recal.table table of scores after recalibration
QC/BAM/BQSR/file_recalibration_plots.pdf before/after recalibration plots

The output_folder directory contains two subfolders: BAM and QC

Directed Acyclic Graph

DAG BQSR

Contributions

Name Email Description
Nicolas Alcala* AlcalaN@fellows.iarc.fr Developer to contact for support