I will provide a complete population genetics analysis from vcf data

Luís Miguel

Portugal

I speak English, Portuguese
I am a bioinformatics researcher currently pursuing a PhD with a focus on functional and population genomics. My work involves genomic data analysis, scripting, and statistical approaches, using tools...
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About this Gig

I will provide a complete population genetics analysis from VCF data, using robust and reproducible methods to characterize genetic diversity, neutrality patterns, and population structure.


Standard analysis includes:

  • Basic VCF statistics and data checks
  • Observed and expected heterozygosity (Ho/He)
  • Inbreeding coefficient
  • Nucleotide diversity (π; genome-wide)
  • Tajimas D (fixed, non-overlapping windows)


Add-on 1: Population-level

Enables population-level analyses using a client-provided sample-to-population mapping file. Includes population-stratified metrics, PCA (LD-pruned), ADMIXTURE (K=210, 3 replicates per K, cross-validation), and pairwise F_ST (genome-wide).


Add-on 2: Sliding Windows

Extends the analysis with genome-wide sliding-window metrics to detect local patterns and outlier windows. Includes π in sliding windows (with step size) and Tajimas D in fixed windows, with plots and tabulated results.

Bonus: If both add-ons are selected, pairwise F_ST is also computed in sliding windows.


Notes: The VCF must contain sample genotypes. Population-level analyses require a mapping file. Dataset size (variants, samples, populations) is limited by the selected package. Outliers refe

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