===Commands===
:::* [[Genome-wide Association-Quality Control Exercise|Genome-wide Association Analysis-Quality Control-PLINK]]:::* [[Genome-wide Association-MDS and PCA Exercise|Genome-wide Association Analysis-MDS and PCA-PLINK]]:::* [[Family-based Association Exercise|Family-based Association Analysis- FaST-LMM, PLINK and R]]:::* [[Mixed models Association Analysis_Exercise|Mixed models Association Analysis Computer – GCTA, PLINK and R]]:::* [[VAT_Exercise|Sequence data quality control and association analysis (VAT)]]:::* [[PSEQ_Exercise|Association Analysis of Sequence Data using PLINK/SEQ (PSEQ)]]:::* [[RV-TDT_Exercise|Rare-Variant Transmission Disequilibrium Test (RV-TDT)]]:::* [[Functional Annotation_Exercise|Functional Annotation]]
===Software===
* [http://www.openbioinformatics.org/annovar/ ANNOVAR]
* [https://github.com/MicrosoftGenomics/FaST-LMM FasT-LLM]
* [https://cnsgenomics.com/software/gcta/ GCTA]
* [https://genome.sph.umich.edu/wiki/MaCH MaCH]
* [https://genome.sph.umich.edu/wiki/METAL METAL]
* [https://genome.sph.umich.edu/wiki/Minimac Minimac]
* [http://zzz.bwh.harvard.edu/plink/ PLINK]
* [https://atgu.mgh.harvard.edu/plinkseq/ PLINK/SEQ
* [https://genome.sph.umich.edu/wiki/RAREMETAL RAREMETAL]
* [[RV-TDT|RV-TDT]]
* [http://bioinformatics.org/spower/ SEQPower]
* [http://varianttools.sourceforge.net/ Variant Association Tools]
This course is supported by a grant from the National Institute of Health (NIH) - National Human Genome Research Institute (NHGRI).