Complex trait genetics Archive

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  • The process for GWAS/WGS

    By Jeff Leek | |

    Brief overview of GWAS and WGS including variant selection, populating stratification, statistical tests, examining locus/fine mapping, and annotation.

  • GWAS and secondary analysis

    By Gina Peloso | |

    Covers GWAS study design, including UK Biobank. Covers QC, both sample and SNP QC, and population structure, imputation (including tools), combining datasets or meta-analysis using summary stats. Also brief overview of a range of secondary analysis including fine mapping, pleiotropy, MR etc.

  • High throughput sequencing and variant calling

    By Geraldine van der Auwera | |

    Discusses exome versus whole-genome sequencing, and the different types of genetic variation that can occur. Introduces tools such as Integrative Genomic Viewer, Burrows-Wheeler Aligner (BWA), STAR Aligner, Picard and GATK. Covers library preparation and sequencing, then data pre-processing (raw sequence output then alignment to reference genome to create BAM file) and variant discovery (for both germline and somatic genetic variation, and also copy number variation).

  • Introduction to complex trait genetics

    By Mark Daly | |

    Covers the evolution of genetics used to understand human disease, from linkage studies right up to the modern-day approach to statistical genetics. A great introduction or refresher.

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