A simple pipeline that takes a freebayes vcf file of biallelic SNPs and an expression matrix in DESeq format and uses two different tests to detect eQTLs. First, we test for allelic imbalance in heterozygous individuals by fitting a beta- binomial distribution for imbalance at each locus and using a likelihood ratio test for deviation from 50-50. Next, we use limma/voom to log transform and calculate precision weights for expression values and use lm to test for associations between genotype and gene expression. P values are calculated using Stouffer's method. Fst and Fst outliers (OutFLANK), Differential expression between populations (DESeq2), and the proportion of population difference in expression explained by eQTLs can be calculated. In addition, functions for plotting expression associations, allelic imbalance, and allele distributions between populations are provided.
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