mutect2

Identify somatic variants in paired-end read DNA sequencing BAM files using GATK4-Mutect2

usage

nexus run --nf-workflow variant_calling_mutect2.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --mutect2_germline_resource_vcf_file /path/to/file.vcf \
    --mutect2_panel_of_normals_vcf_file /path/to/file.vcf \
    --getpileupsummaries_variant_vcf_file /path/to/file.vcf \
    --params_gatk4mutect2 "" \
    --params_gatk4getpileupsummaries "" \
    --chromosomes "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY,chrM"

Note

Nextflow config files are available here. Use the config file that matches your installed nexus version (e.g. nexus_v0.2.0_nextflow_slurm.config).

parameters

parameter	description
--samples_tsv_file	TSV file with the following columns: ‘sample_id’, ‘tumor_bam_file’, ‘tumor_bam_bai_file’, ‘normal_bam_file’, ‘normal_bam_bai_file’, ‘normal_sample_id’.
--output_dir	Directory to which output files will be symlinked.
--reference_genome_fasta_file	Reference genome FASTA file.
--mutect2_germline_resource_vcf_file	Germline resource VCF file. This VCF file will be supplied to gatk Mutect2 –germline-resource parameter.
--mutect2_panel_of_normals_vcf_file	Panel of normals VCF file. This VCF file will be supplied to gatk Mutect2 –panel-of-normals parameter.
--getpileupsummaries_variant_vcf_file	GetPileupSummaries variant VCF file.
--params_gatk4mutect2	GATK4 Mutect2 parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes.
--params_gatk4getpileupsummaries	GATK4 GetPileupSummaries parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes.
--chromosomes	Chromosomes to parallelize (default: ‘chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY,chrM’).