General codes and scripts for key steps in HSCR WES analysis

Sample selection

• case: selectVariant_bysample.sh
  
• control: FlashPCA.sh & UKB_ctrl_selection_PCdistance.ipynb (control selection based on PCA)
  

Bioinformatics procedures

• WES alignment with Burrows-Wheeler Aligner (BWA-MEM): align_bwa_mem_broad.sh
  
• Variant calling with GATK-HaplotypeCaller
  o gVCF.sh
  o different ploidy for males and females on sex chromosomes when generating gVCF: gVCF_sexchr_male_chrX_nonPAR.sh
  
• Variant QC
  o VQSR: VQSR.sh
  o Hard filter: variantannot_hard_filter.sh
  o 10% missing genotype filter: missingness_filter.sh
  o Contamination
     • verifyBamID: verifybam.sh
     • Haplocheck: haplocheck.sh
  o GATK’s CollectVariantCallingMetrics: vcfQC.sh
  o GAKT’s GenotypeConcordance: GenotypeConcordance.sh
  
• Family-based de novo Mutation Calling: per_fam_DNM.sh
  
• Sample QC for Sex.
  o read depth on the sex differential SRY gene region: sex_check_SRY.sh
  o reads ratio on chrY versus chrX, normalized by the total reads for each sample: sex_check_ratio.sh
  
• Sample QC for Relatedness: relatedness.R & relatedness.R.sh
  
• Ancestry and Admixture Analysis: plink_admixture.sh
  
• Variant functional annotation
  o Ensembl Variant Effect Predictor (VEP): vep.sh
  o Pathogenicity prediction
     • phylop241way: phylop241.sh
     • VEST4: https://www.cravat.us/CRAVAT/help.jsp
     • LOFTEE : vep_LOFTEE.sh & vep_annot_parse.ipynb
     • spliceAI: https://github.com/Illumina/SpliceAI
     • REVEL: https://sites.google.com/site/revelgenomics/downloads?authuser=0
     • metaRNN: metaRNN.sh
     • gnomadAD AF: gnomadv4_AF_by_population.sh
  
• Human Embryonic Gut Gene Expression: Seurat: scRNAseq_gut.R
  

Statistical analysis

• Firth logistic regression: logit_firth.R & logit_firth.sh
  
• Bootstrapping: bootstrapping.R & bootstrapping.R.sh
  
• SKAT-O: SKAT.R & SKAT.R.sh
  
• Inflation factor: qqperm.R & qqperm.R.sh
  
• de novo Analysis: DNM.R
  
• Joint-analysis with extTADA: https://github.com/hoangtn/extTADA