Population Genomics & Evolutionary Modeling — Hands-on

Gain expertise in population genomics and evolutionary modeling—QC, structure, demography, selection scans, and reproducible reporting for research and clinical cohorts.

Population Genomics & Evolutionary Modeling

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Session Index

Session 1 — Study Design, VCF QC & Kinship Session 2 — Structure: PCA, ADMIXTURE & FST Session 3 — Demography, Selection & Phylodynamics Session 4 — Mini Capstone: PopGen Pipeline

Session 1

Fee: Rs 6300

Study Design, VCF QC & Kinship

Cohort design, sequencing choices, metadata & consent schemas

Theory

VCF QC, filtering and missingness/LD pruning workflows

bcftools vcftools PLINK 1.9/2.0

Relatedness, IBD/IBS, ROH and pedigree checks

KING PLINK --ibd/--homozyg IBDseq

Session 2

Fee: Rs 8400

Structure: PCA, ADMIXTURE & FST

Dimensionality reduction and population stratification

PCA (EIGENSOFT) PCAngsd

Global/local ancestry and admixture proportions

ADMIXTURE fastSTRUCTURE fineSTRUCTURE

Differentiation and gene flow modeling

F_ST Treemix f3/f4/qpAdm

Session 3

Fee: Rs 11200

Demography, Selection & Phylodynamics

Demographic inference from whole genomes

PSMC/MSMC/SMC++ ∂a∂i (dadi) fastsimcoal2

Selection scans and linked selection signals

iHS/XP-EHH CMS/SDS SweepFinder2 LDhelmet

Coalescent phylogenetics and species delimitation

BEAST BPP SNAPP

Session 4

Fee: Rs 14000

Mini Capstone: PopGen Pipeline

Design an end-to-end popgen pipeline with full provenance

Theory

Automate QC→structure→demography→selection→report steps

Snakemake Conda/Mamba Quarto/JupyterLab

Deliver figures/tables and submission-ready metadata (SRA/GEO/ENA)

pandas plotly PLINK/ADMIXTURE

Population Genomics & Evolutionary Modeling Training | Structure, Demography & Selection Scans

Hands-on population genomics: VCF QC, kinship, PCA, ADMIXTURE, FST/IBD, demographic inference (PSMC/MSMC, dadi) , selection scans (iHS, XP-EHH) , Treemix, reproducible pipelines.

Population Genomics & Evolutionary Modeling — Hands-on