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AM edited this page Aug 6, 2019 · 10 revisions

Step-by-step instructions of various genetic analyses

Reading VCF file into GDS format and understanding the GDS format
https://uw-gac.github.io/SISG_2019/gds-format.html

Generate genotype principal components in the presence of relatedness
https://uw-gac.github.io/SISG_2019/pc-relate.html

Association tests
https://uw-gac.github.io/SISG_2019/association-tests.html

Concepts and protocols for data quality control in genome-wide association study
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025522/

Estimate global ancestry using admixture
https://github.com/asthmacollaboratory/Resources/wiki/Estimate-global-ancestry-using-admixutre

Estimate local ancestry using LAMPLD
https://github.com/asthmacollaboratory/Resources/wiki/Estimate-local-ancestry-using-LAMPLD

Other resources

Tools to manipulate VCF/BCF files
https://samtools.github.io/bcftools/bcftools.html