bio-population-genetics-selection-statistics
GPTomicsDetect signatures of natural selection using Fst, Tajima's D, iHS, XP-EHH, and other selection statistics. Calculate population differentiation, test for departures from neutrality, and identify selective sweeps with scikit-allel and vcftools. Use when computing selection signatures like Fst or Tajima's D.
bio-population-genetics-scikit-allel-analysis
GPTomicsPython population genetics with scikit-allel. Read VCF files, compute allele frequencies, calculate diversity statistics, perform PCA, and run selection scans using GenotypeArray and HaplotypeArray data structures. Use when analyzing population genetics in Python.
bio-population-genetics-linkage-disequilibrium
GPTomicsCalculate linkage disequilibrium statistics (r², D'), perform LD pruning for population structure analysis, identify haplotype blocks, and visualize LD patterns using PLINK, scikit-allel, and LDBlockShow. Use when calculating LD or pruning variants.
bio-population-genetics-association-testing
GPTomicsGenome-wide association studies (GWAS) with PLINK. Perform case-control and quantitative trait association testing using logistic/linear regression with covariates, generate Manhattan and QQ plots for result visualization. Use when running GWAS or association tests.
bio-population-genetics-population-structure
GPTomicsAnalyze population structure using PCA and admixture analysis with PLINK and ADMIXTURE. Identify population clusters, assess ancestry proportions, visualize genetic structure, and choose optimal K for admixture models. Use when analyzing population stratification with PCA or admixture.
bio-variant-calling-joint-calling
GPTomicsJoint genotype calling across multiple samples using GATK CombineGVCFs and GenotypeGVCFs. Essential for cohort studies, population genetics, and leveraging VQSR. Use when performing joint genotyping across multiple samples.
bio-population-genetics-plink-basics
GPTomicsPLINK file formats, format conversion, and quality control filtering for population genetics. Convert between VCF, BED/BIM/FAM, and PED/MAP formats, apply MAF, genotyping rate, and HWE filters using PLINK 1.9 and 2.0. Use when working with PLINK format files or running QC.
claw-ancestry-pca
manuelcorpasAncestry decomposition PCA against the Simons Genome Diversity Project
claw-ancestry-pca
ClawBioAncestry decomposition PCA against the Simons Genome Diversity Project