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Welcome to the mixqtl wiki!

mixQTL, mixFine, and mixPred form a suite of methods that perform cis-QTL, fine-mapping, and prediction of gene expression traits integrating total read count and allele-specific expression. They leverage a log-linear modeling of read counts to accelerate the calculation.

There are three main R functions that perform the necessary calculations: mixqtl, mixfine, and mixpred. Here we explain how to use each of these functions.

For those who prefer to work from the command line, we provide a command line tool that facilitates the performance of mixQTL across the full transcriptome. The tool takes phased genotypes, total, and allele specific read counts to cis-QTL mapping analysis across the full transcriptome. A tutorial can be found here with explanation of input formats, output formats and command-line arguments.

A computationally efficient GPU-based implementation of mixQTL is embedded in the tensorQTL software here