Organizer: H3ABioNet

Host institution: H3ABioNet

Start: Monday, 27 August 2018 @ 15:00

End: Monday, 27 August 2018 @ 16:00

Timezone: Central African Time (CAT)

Sponsors: H3ABioNet

Contact: info@h3abionet.org

Scientific topic: Population genomics, Bioinformatics, Genotyping experiment, Genomics, Computational biology

Target audience:
  • Anyone intersted in GWAS and using the H3Africa genotyping chip
Description:

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.

Event type:
  • Workshops and courses

Capacity: 150

Keywords: Genotype calling, H3ABioNet, Genotype calling, Genome Studio, H3Africa genotyping array, African populations, Array processing, Illumina arrays, File formats, Annotations, Non-polymorphic, Top/Bottom annotation, Genotype array probes, Intensities, Convert to PLINK format , Bioinformatics, Genome Wide Association Studies

H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 3 https://tess.elixir-europe.org/events/h3abionet-2018-genotyping-chip-data-analysis-and-gwas-lecture-series-lecture-3 ### 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. 2018-08-27 15:00:00 UTC 2018-08-27 16:00:00 UTC H3ABioNet Population genomics Bioinformatics Genotyping experiment Genomics Computational biology H3ABioNet info@h3abionet.org H3ABioNet Anyone intersted in GWAS and using the H3Africa genotyping chip 150 workshops_and_courses [] Genotype callingH3ABioNetGenotype callingGenome StudioH3Africa genotyping arrayAfrican populationsArray processingIllumina arraysFile formatsAnnotationsNon-polymorphicTop/Bottom annotationGenotype array probesIntensitiesConvert to PLINK format BioinformaticsGenome Wide Association Studies