SAIGE-QTL is an R package developed with Rcpp for scalable and accurate expression quantitative trait locus (QTL) mapping for single-cell studies.

The method

  • Models repeated and complex data structure, due to multiple cells per individual and relatedness between individuals
  • Models discrete read counts
  • Is fast and scalable for large data, can test 20k genes, tens to hundreds of cell types, millions of cells, millions of genetic variants
  • Can test for the effects of rare variation, for which the single-variant test is underpowered (uses set-based tests instead).

The package takes genotype file input in the following formats

  • PLINK (bed, bim, fam), BGEN, VCF, BCF, SAV

Please note that accounting for total read counts per cell is critical in single-cell eQTL mapping. The SCTransform in the SCTransform function in the Seurat R package and/or including log(total read counts) and percentage of MT read counts for each cell as covariates in the Step 1 null model can be used.


Please find logs for bugs fixed



  • preprint coming out soon!


SAIGE-QTL is distributed under an MIT license.


If you have any questions about SAIGE-QTL please contact