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UNDER DEVELOPMENT

  • I have removed all scripts to redevelop and redeploy this repository as a one-stop, organized, updated, and simple-to-follow GWAS tutorial.
  • It will contain the tips and tricks that I have accumulated throughout my experience in analyzing highly diverse African populations.




WATCH OUT FOR UPDATES!!!


Pipeline (Workflow)

Pre-QC Association analysis

  • Model: Logistic (95% confidence interval), 1df Chi square allelic test (adjusted to assess the genomic control inflation factor - λ).
  • Mode of inheritance (MOI): Additive, Recessive, HetHom, Allelic and Genotypic,
  • Tools: PLINK1.9, SNPTEST, R

Sample (per individual) QC

  • Identification of individuals with discordant sex information.
  • Identification of individuals with high missing values or outlying heterozygosities.
  • Identification of duplicate or related individuals or individuals of divergent ancestry
  • Tools: QCTOOL, PLINK1.9, R

SNP (per marker) QC

  • Identification of SNPs with excessive missing genotype
  • Exclusion of rare SNPs (MAF < 1%)
  • Identification of SNPs demonstrating significant deviation from HWE
  • Identification of SNPs with significant differential genotyping call rate between cases and controls
  • Tools: PLINK1.9, R

Population Structure Determination

  • Multidimensional scaling (eliminate population outliers)
  • Principal component analysis with 10 axes of genetic variation (principal components)
  • Fst and Haplotype based fine structure analysis
  • Tools: Plink1.9, EIGENSOFT, fsStructure, ChromoPainter, GLOBETROTTER, R

Haplotype Estimation (phasing)

  • SHAPEIT2, Eagle2

Genotype Imputation

  • IMPUTE2, PBWT, MINIMACH

Post-Imputation Association analyses

  • Models: Logistic regression, Linear mixed models (LMM)
  • Modes of inheritance: dominant, recessive, heterozygous, additive, allelic
  • Tools: PLINK1.9, SNPTEST2, R

Follow-up Imputation of putative associations

  • Phasing with IMPUTE2 MCMC approach
  • Imputation with IMPUTE2

Association analysis

  • Models: Logistic regression, Linear mixed models (LMM)
  • Modes of inheritance (MOI): dominant, recessive, heterozygous, additive, allelic
  • Tools: PLINK1.9, SNPTEST2, R

License

Creative Commons Licence
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.