iderare_example.yml

analysis:
  # Full Path of trio data
  data_dir: /home/ivanwilliamharsono/Downloads/trio_patient

  # Note :
  # 1. Ensure all proband, father, mother saved on the same path
  # 2. Ensure file name is cleaned .fq.gz, if your file is raw untrimmed fastq, adjust pipeline_template.sh, uncomment Step 0
  # 3. Insert proband, mother, father file name (not full path) without .fq.gz file
  # 4. File should be prepared on {data_dir}/input/A_FASTQ
  # This data source follow the original data sourced from this link : https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=1077459
  proband: V350145665_L04_B5EHOMdmhwXAAAA-515
  mother: V350145665_L04_B5EHOMdmhwXAABA-517
  father: V350145665_L04_B5EHOMdmhwXAACA-519

  # Gender setting 1=male, 2=female, 0=unknown
  # Proband Gender
  proband_gender: 1

  # Phenotype -9=missing, 0=missing; 1=unaffected; 2=affected
  proband_phen: 2
  mother_phen: 1
  father_phen: 1

  # HPO IDs of patient
  hpo_ids:
  - HP:0000007
  - HP:0001433
  - HP:0001903
  - HP:0001541
  - HP:0010972
  - HP:0005561
  - HP:0001396
  - HP:0001410
  - HP:0002910
  - HP:0001399
  - HP:0000938
  - HP:0001653
  - HP:0200114
  - HP:0003073
  - HP:0003233
  - HP:0001873
  - HP:0002151
  - HP:0031964
  - HP:0031956
  - HP:0002366
  - HP:0006568
  - HP:0004333
  - HP:0001531

  # Library Name - Any kind of sequencing method (e.g. AgilentV6)
  library: AgilentV6
  # Method - Any kind of sequencing method (e.g. DNBSeq)
  method: DNBSeq

setup:
  # deep variant version #1.5.0 - tested for GPU <8GB | v1.6.0 need minimum GPU memory of 16 GB
  dv_version: 1.5.0

  # glnexus and tiddit docker version
  glnexus_version: 1.4.1
  tiddit_version: 3.6.1--py38h24c8ff8_0

  # deep variant model (WES/WGS)
  dv_model: WES

  # max memory allowed (G = Gigabyte)
  max_mem: 60G

  # refseq directory (full folder), assuming you save it on Downloads/Database
  ref_dir: /home/ivanwilliamharsono/Downloads/Database
  # refseq fasta file name (file name)
  ref_fasta: hg38.p14.fa

  # SnpEff data directory & version
  snpEff_dir: /home/ivanwilliamharsono/Downloads/Sandbox/snpEff/data
  snpEff_ver: GRCh38.p14

  # Exomiser data directory & version
  exomiser_dir: /home/ivanwilliamharsono/Downloads/Sandbox/exomiser/data/exomiser-data
  exomiser_data_ver: 2309

  #dbNSFP file
  dbNSFP_file: /home/ivanwilliamharsono/Downloads/Database/dbNSFPv4.5a_custombuild.gz

  #dbSNP file
  dbSNP_file: /home/ivanwilliamharsono/Downloads/Database/Homo_sapiens_assembly38.dbsnp156_snpsift.fixed.vcf.gz

  #ClinVar file
  ClinVar_file: /home/ivanwilliamharsono/Downloads/Database/clinvar_20240215.vcf.gz

  # SnpSift adjuster
  chr_rename: /home/ivanwilliamharsono/Downloads/IDeRare/convert/vcf_rename.chrnames