BQSR-nf

Nextflow pipeline for base quality score recalibration with GATK processing

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

Contributions

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