Does GENESIS support using imputed dosages instead of discrete genotype calls in association tests?

GENESIS does support imputed dosages, but if you are starting with VCF files there is an extra conversion step involved to get this to work.

For imputed dosages in VCF format, use the SeqArray package:

1. use seqVCF2GDS to convert your VCF file to a SeqArray GDS file
2. use seqGDS2SNP with the argument dosage=TRUE to convert that file to a GDS format supporting dosage in the "genotype" node

For imputed dosages in other formats (IMPUTE2, BEAGLE, MACH), use the GWASTools package:

1. use imputedDosageFile to convert directly to a GDS file with dosage in the "genotype" node

Finally, use the GWASTools package to create a GenotypeData object for use in GENESIS. See the vignette for an example of running association tests with GenotypeData objects: https://bioconductor.org/packages/devel/bioc/vignettes/GENESIS/inst/doc/assoc_test.html

In the next development cycle, we plan to add support for reading dosages directly from SeqArray GDS files.

As of version 2.13.2, GENESIS supports the use of imputed dosages directly from SeqArray GDS files in association testing. Convert a VCF with imputed dosages preserving the dosage field:

seqVCF2GDS(vcffile, gdsfile, fmt.import="DS")

Then run assocTestSingle or assocTestAggregate with option imputed=TRUE.

SeqVarTools version 1.21.1 or later is required to use this feature.