config.yaml

---
# References
PATH_hg38: "/path/to/hg38.fa"
PATH_hg38_dict: "path/to/hg38.fa.dict"
PATH_bed: "/path/to/targeted_sequencing_bed_file.bed"
PATH_bed_intervals: "/path/to/bed.interval_list"
PATH_baits: "/path/to/panel_baits.interval_list"

# For base recalibration
PATH_known_indels: "/path/to/resources_broad_hg38_v0_Homo_sapiens_assembly38.known_indels.vcf"
PATH_gold_std_indels: "/path/to/resources_broad_hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf"
PATH_SNP_db: "/path/to/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf"

# For Mutect2
PATH_PoN: "/path/to/pon.vcf.gz"

# Data files
DIR_results: "results"
DIR_fastq: "results/data/fastq"
DIR_bams: "results/data/bam"
DIR_recalibrated_base_scores: "results/base_recalc_info"

# Fastqc reports
DIR_fastqc: "results/reports/fastqc/merged" # running fastqc right after merging individual fastqs from lanes

# Metrics outputs
DIR_umi_metrics: "results/metrics/umi_metrics"

# Variant calling and annotation
DIR_Vardict: "results/variant_calling/Vardict"
DIR_Mutect: "results/variant_calling/Mutect2"
DIR_freebayes: "results/variant_calling/freebayes"
DIR_ANNOVAR: "results/data/annovar_outputs"

# Metrics
DIR_metrics: "results/metrics"