Whole-Exome-Sequencing-WES-Data-Analysis-Pipeline/ngs_config.yaml at main · Waqaskhan600/Whole-Exome-Sequencing-WES-Data-Analysis-Pipeline · GitHub

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# NGS Pipeline Configuration
project_name: "Basic WES NGS Pipeline"
description: "A standardized configuration for Whole Exome Sequencing analysis."

# Paths and Directories
project_dir: "/media/user/New_Volume/ngs"
directories:
  input_data: "${project_dir}/input"
  results_dir: "${project_dir}/results"
  qc_dir: "${project_dir}/results/qc"
  trimmed_dir: "${project_dir}/results/trimmed"
  reference_genome: "${project_dir}/resources/reference/hg38.fa"
  known_sites_dbsnp: "${project_dir}/resources/reference/Homo_sapiens_assembly38.dbsnp138.vcf.gz"
  known_sites_indels: "${project_dir}/resources/reference/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"
  target_regions: "${project_dir}/resources/reference/target_regions.bed"
  target_intervals: "${project_dir}/resources/reference/target_regions.interval_list"

# Sample Information
samples:
  - id: "demo_1"
    fastq_r1: "${project_dir}/input/demo_1_R1.fastq.gz"
    fastq_r2: "${project_dir}/input/demo_1_R2.fastq.gz"

# Hardware / Processing
execution:
  threads: 6
  memory_gb: 16

# Tool-specific parameters
trim_galore:
  quality: 20
  length: 20

gatk:
  variant_filtration:
    - name: "LowQD"
      expression: "QD < 2.0"
    - name: "HighFS"
      expression: "FS > 60.0"
    - name: "LowMQ"
      expression: "MQ < 40.0"
    - name: "HighSOR"
      expression: "SOR > 3.0"
    - name: "LowMQRankSum"
      expression: "MQRankSum < -12.5"
    - name: "LowReadPosRankSum"
      expression: "ReadPosRankSum < -8.0"
    - name: "LowDepth"
      expression: "DP < 20"
    - name: "HighDepth"
      expression: "DP > 500"