Mutect2 Panel of Normals Workflow

Nextflow implementation for Mutect2 Panel of Normals subworkflow, based on latest Mutect2 Best Practices guidelines

Quick Start

Required Arguments:

argument	value
normal_bam_folder	a path to the input folder with bam and .bai files
ref	a path to the unzipped fasta reference file, used to map the bam files
ref_index	a path to fasta.fai index of the reference reference file, used to map the bam files
ref_dict	a path to the .dict file generated from the fasta reference file
interval_list	a path to the interval list file, with coordinate ranges defined per line as chr:start-end, must have suffix .list
af_only_gnomad_vcf	a path to the external resource unzipped vcf file found here from the Genome Aggregation Database (gnomAD).
af_only_gnomad_vcf_idx	a path to the external resource unzipped vcf file index generated with gatk IndexFeatureFile .

To test the pipeline with your input folder of bam files you can run:

# Clone the repository
git clone https://github.com/cgpu/Mutect2PanelofNormalsWorkflow-nf

# cd into the repo folder 
cd Mutect2PanelofNormalsWorkflow-nf

# Execute nextflow run command with example input parameters
nextflow main.nf \ 
--normal_bam_folder path/to/input/folder/  \ 
--ref ref.fasta \ 
--ref_index ref.fasta.fai \ 
--ref_dict  ref.dict\ 
--interval_list WES_interval.list \ 
--af_only_gnomad_vcf  af-only-gnomad.raw.sites.hg19.vcf \ 
--af_only_gnomad_vcf_idx  af-only-gnomad.raw.sites.hg19.vcf.idx \ 
-with-docker broadinstitute/gatk:latest