Association Tests
This kind of association does not require the removal of outliers. It uses the Cochran-Mantel-Haenszel (CMH) association statistic to do an association test conditional on the matching done in the population stratification step. The clustering uses Plink’s Inheritance-by-Structure (IBS) clustering.
This kind of association uses a general association test, and assumes that outliers have been removed following an appropriate process.
Copy Number Variation (CNV) Detection
This workflow combines results from the GNOSIS CNV detection algorithm and PennCNV detection algorithm (including X-Chromosome detection) to produce a file containing Merged CNVs. It then processes these further to compare the results with a list of Common CNVs, and assesses the overlap of parent and children CNVs. Finally it annotates the results.
This workflow combines results from the GNOSIS CNV detection algorithm and PennCNV detection algorithm to produce a file containing Merged CNVs. It then processes these further to compare the results with a list of Common CNVs, and assesses the overlap of parent and children CNVs. Finally it annotates the results.
This workflow combines results from the GNOSIS CNV detection algorithm and PennCNV detection algorithm (including X-Chromosome detection) to produce a file containing Merged CNVs. Finally it annotates the results.
This workflow combines results from the GNOSIS CNV detection algorithm and PennCNV detection algorithm to produce a file containing Merged CNVs. Finally it annotates the results.
This workflow uses the GNOSIS CNV detection algorithm to detect CNVs and then annotates the results.
This workflow uses the PennCNV CNV detection algorithm to detect CNVs and then annotates the results.
Variant Discovery
This workflow detects variants via resequencing. It uses the BWA Tool (Burrows-Wheeler Alignment Tool) and then SAMTools (Sequence Alignment/Map tools) to accomplish this.
Family-based Association Analysis (TDT)
This is basic family-based association testing for disease traits, using the TDT function in PLINK
This is variant of the basic family-based association testing for disease traits that also incorporates parental phenotype information, the ParenTDT function in PLINK
Structure Workflow
This workflow converts Pedigree Data to Structure format, and then runs STRUCTURE on it