ValdmanisLab/LocalAncestry_APOE-APOC1_AFR

Local African Ancestry at APOE/APOC1 using 1KGP # Local African Ancestry Prediction Pipeline (Chr19 APOE-APOC1) using 1KGP ## Overview This pipeline predicts local African ancestry (AFR vs. non-AFR) using SNP data from chromosome 19. The model is trained on 1000 Genomes Project samples and can be applied to any external VCF file overlapping the trained SNP positions. The focus region for SNP extraction is: **chr19:44903121–44921336**. --- ## Input Files and Structure All files are organized under: ### Folder Structure - `data/Files_to_prepare_the_model/` - `chr19_44903121_44921336_1KGP.vcf.gz`: Extracted VCF file for the APOE region on chromosome 19 from the 1000 Genomes Project. - `chr19_44903121_44921336_1KGP.vcf.gz.csi`: CSI index file for the corresponding VCF. - `snp_positions_chr19_44903121_44921336.tsv`: List of selected SNPs (CHROM, POS) used to build and filter the model input features. - `igsr_samples.tsv`: Metadata file containing sample names and superpopulation labels (AFR, EUR, EAS, SAS, AMR). - `list_of_no_relatives_1KGP.tsv`: Filtered list of unrelated samples from the 1000 Genomes Project used for model training. - `code/` - `LocalAncestry_APOE-APOC1_AFR.ipynb`: Main Jupyter notebook implementing the end-to-end local ancestry prediction pipeline. - `results/` - `Model/`: Folder where the trained model (`.pkl`) and SNP importance table (`.tsv`) are saved. - `Graphs/`: Contains visual outputs such as confusion matrix, PCA plot, and ROC curve. --- ## Model Methodology - **Model Type**: Random Forest Classifier (`sklearn.ensemble.RandomForestClassifier`) - **Parameters**: - `n_estimators=200` - `max_depth=15` - `min_samples_leaf=2` - `class_weight='balanced'` - **SNP Features Used**: 205 SNPs common between model list and input VCF - **Genotype Encoding**: - 0 = homozygous reference (e.g., A\|A) - 1 = heterozygous (e.g., A\|G or G\|A) - 2 = homozygous alternative (e.g., G\|G) - -1 = missing/uninterpretable - **Filtering Criteria**: - SNPs retained if ≥90% of samples have valid genotype …