Genotype_calling_from_chip_data_Lecture_3.pdf (2.05 MB)

Genotype calling from chip data - Lecture 3 H3ABioNet 2018 GWAS Lecture series

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posted on 11.09.2018 by Ayton Meintjes

Genotype calling from Illumina files

The third of a series of seven H3ABioNet online lectures for Genome Wide Association Studies (GWAS) will introduce genotyping SNP array chips with particular emphasis on the H3Africa genotype chip. The lecture will cover common file formats when obtaining genotyping chip data from a service provider such as Illumina and software used for genotype calling. This lecture will also cover genotype calling, sample and probe quality control, probe viewing and exporting of data using GenomeStudio. Converting the data to PLINK format and some tips on troubleshooting and common pitfalls will be discussed.


Research reported in this publication was supported by the National Human Genome Research Institute of the National Institutes of Health under Award Number U24HG006941. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.