Recently I have come cross some illumina ominzhonghua genotype idat file. How can I parse these idat files.
I have tried to use the R package of illuminaio with the following code. However, I don't know how to get the allele type for each SNPs.
library("illuminaio")
idat1
Illuminaio is a package only for extracting the information encrypted in IDAT files. It is not designed for calling genotypes or performing other downstream analyses.
For that, there is a Bioconductor package called crlmm that can be used for processing IDAT data, calling genotypes, and several other analysis steps. However, for genotyping, crlmm requires an annotation package specific to the platform in use. And as I see it, this annotation is not yet available for the HumanOmniZhongHua-8.
To my knowledge, under that circumstances you will be forced to use Illumina's own software (GenomeStudio, genotyping module) for genotype calling. However, this is a commercial software and you would need to buy a licence..
Do you guys know what "MidBlock" stands for? It has the same length as the number of probes but I don't see whether this is important. At least, illuminaio vignette does not comment on it.
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