Overview of the reference files

References, panel of normals and design files used by the pipeline are listed below. They are defined in the config/config.yaml file and can be found in the ref_data/ folder of the project.

config entry / rule	sub-entry	file	description
reference	fasta	GRCh38.fasta	Reference genome in FASTA format
	fai	GRCh38.fasta.fai	Index file for the reference genome
	trf	GRCh38.trf.bed	Human tandem repeats (used by Severus and PBSV)
	design_bed	expected_coverage_annotated.bed	BED file with panel target regions
	sv_databases	gnomad.v4.1.sv.sites.no_cnv.PASS.vcf.gz, sv_normal.vcf.gz	Population SV VCF files queried directly by SVDB. List — add new population databases here.
cnvkit_batch	normal_reference	cnvkit.PoN.cnn	Panel of normals for CNVkit
deepsomatic_t_only	pon	snv_normal.vcf.gz	Panel of normals for DeepSomatic (used when use_deepsomatic: true)
severus_t_only	pon	PoN_1000G_hg38.tsv.gz	Panel of normals for Severus (1000 Genomes project)
	vntr	GRCh38.trf.bed	Tandem repeat BED file passed to Severus via --vntr
bcftools_filter_include_region	panel	expected_coverage_annotated.bed	Regions to include in variant calling
general_report		config/report.yaml	General report configuration file