PigGTEx_v0 - Analysis Pipeline

This repository contains analysis pipelines used by the pilot phase (V0) of PigGTEx project, including:Whole-genome sequence alignment, SNP calling, and quality controlRNA-seq alignment, quantification, SNP calling, genotype imputation, and quality controlTissue-specific gene expression and co-expression analysisBioinformatics analysis of WGBS dataSingle-cell RNA-Seq analysisBreed prediction for RNA-Seq samplesCis-heritability estimation for gene expressionMolecular QTL (molQTL) mapping, meta-analysis, effect size measurement, and evolutionary conservationAllele-specific expression (ASE) analysisFunctional annotation (snpEff and chromatin state) of molQTLInterpreting GWAS loci with molQTL: enrichment, expression-mediated heritability, transcriptome-wide association study, Mendelian Randomization, and co-localizationComparative analysis between pig and human