Illumina Exome Chip Prcessing and Quality Control Protocols


The exome genotyping array was introduced as an affordable alternative to exome sequencing. Two major exome genotyping arrays are currently commercially available: The Illumina Infinium HumanExome BeadChip array and the Affymetrix Axiom Exome array. Each approach offers slightly different marker selection variation and customizability. In the present protocol, we will focus on the Illumina Infinium HumanExome BeadChip array, hereafter referred as exome chip.


The detailed protocols and scripts can be found at github.

MerrimanLab updated the protocols in 2016, also avaiable at github.


Guo Y, He J, Zhao S, Wu H, Zhong X, Sheng Q, Samuels DC, Shyr Y, Long J: Illumina human exome genotyping array clustering and quality control. Nature Protocols 2014, 9(11):2643-2662.