All Pipeline Steps
Click on any step to view detailed documentation including technical overview and chronological activity log
1
Sample Missingness Filter
Dec 15
Remove high-missingness samples (F_MISS > 0.20). Result: 1,247 → 1,155
✓ Completed
2
IBD Deduplication & Removal
Dec 16
Identify and remove IBD-related duplicates. Result: 1,155 → 1,098 samples.
✓ Completed
3
SNP QC & VCF Export
Dec 17
Variant-level QC (call rate, HWE, MAF) and conversion to VCF for imputation. 654K → 473K variants.
✓ Completed
4
Michigan Imputation Server
Dec 18–22
Phasing (Eagle2) + imputation (Minimac4) against TOPMed r2. 473K → 10.8M variants.
✓ Completed
5
ID Normalization
Dec 23
Harmonize sample IDs between genotype array and imputed dataset. Validate 1,098-sample merge.
✓ Completed
6
Final QC & Output
Dec 26
Post-imputation QC (R²≥0.3, MAF, HWE). Final dataset: 1,074 samples, 10.1M variants.
✓ Completed
7
Local PCA Analysis
Jan 3–4
PLINK PCA on UZB cohort. PC1 vs PC2 scatter, outlier removal, population stratification assessment.
✓ Completed
8
Global PCA + 1000 Genomes
Jan 4
Project UZB onto 1000G reference panel. Ancestry inference: broad Central Asian cluster between EUR and SAS/EAS.
✓ Completed
9
FST Analysis (UZB vs EUR)
Oct–Nov
Genome-wide Weir & Cockerham FST UZB vs 1000G EUR. Weighted FST = 0.020. Top outlier regions identified.
✓ Completed
10
Multi-Population Analysis & PBS
Feb 16
PBS multi-pop FST, delta-AF vs EUR/EAS/SAS/AFR. 8 Uzbek-specific SNPs identified. ADMIXTURE K=2–8 complete.
✓ Complete
11
ADMIXTURE K=2–8 Analysis
Mar 2026
Unsupervised ADMIXTURE on UZB + all 2,548 1000G. K=5 most parsimonious (CV=0.295); sNMF validated. Interactive stacked-bar plots.
✓ Complete
12
PBS SNP Functional Annotation
Mar 2026
Ensembl VEP annotation of 490 Uzbek-specific PBS candidates. 264 unique genes; 5 missense variants (4 damaging incl. SPI1, SLC6A2). HLA/MHC over-represented.
✓ Complete
13
LD Clumping & Decay Analysis
Mar 2026
PLINK LD clumping reduced 490 PBS candidates to 401 independent loci. LD decay from r²=0.096 at 0 kb to plateau ~0.011 at 200 kb+. Chr6/MHC: 135 loci (33.7%).
✓ Complete
14
FST Heatmap & MDS
Mar 2026
Full 5×5 pairwise FST matrix (UZB, EUR, EAS, SAS, AFR). Interactive heatmap + classical MDS. UZB closest to SAS (0.018), then EUR (0.020). All values match published 1000G ranges.
✓ Complete
15
ROH & IBD Analysis
Mar 2026
36,702 ROH segments across 1,047 individuals. Median FROH=0.015 (comparable to outbred populations). IBD reveals 6,368 pairs (PI_HAT≥0.05), minimal close relatedness. Critical for pregnancy loss GWAS design.
✓ Complete
→
Next Steps: Planned Analyses
Mar 28
ROH, DAPC, pregnancy loss GWAS design (April 2026), covariates, case/control criteria.
📋 Roadmap
Daily Activity Logs
Daily logs with terminal command history and execution details from Biotech2024 workserver.
Workserver Connection
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config.json
PCA Viewer (Enhanced)
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