SNP & Variation Suite Tutorials

Learn how to use and integrate Golden Helix SVS with step-by-step tutorials on new features, key workflows, and advanced techniques. This page is just getting started. If you find these tutorials helpful and would like to see a tutorial added please let us know. We'd be happy to accommodate!


WHOLE GENOME COPY NUMBER ASSOCIATION WORKFLOW

This tutorial shows you how to perform whole genome copy number association studies with CNAM and HelixTree. You learn how to import and normalize data, correct for batch effects/stratification, filter markers, identify copy number variations (CNVs), and perform association analysis with copy number segments and LogRs.

WHOLE GENOME HOMOZYGOSITY ASSOCIATION

This tutorial shows you how to perform whole genome homozygosity association with HelixTree. As discussed in Lencz, 2008, you learn how to identify runs of homozygosity (ROHs) and perform association on ROH covariates.

FAMILY-BASED COPY NUMBER VARIATION ASSOCIATION

This tutorial shows you how to perform family-based copy number association studies using Golden Helix PBAT. You learn how to properly import and format copy number and pedigree data and perform FBATs on LogRs.

DETERMINING THE CORRECT NUMBER OF PRINCIPAL COMPONENTS TO USE FOR PCA ANALYSIS

This tutorial covers a simple heuristic to help you determine the correct number of principal components to use to correct for batch effects and population stratification. For both SNP and CNV analysis you learn how to compute and plot the log of eigenvalues and then use HelixTree's segmenting algorithm to find the position of the "elbow" on a a scree plot.

VISUALIZE COPY NUMBER VARIATION IN AFFYMETRIX GENOME BROWSER

This tutorial shows you how to visualize LogRs and copy number segmentation results in Affymetrix's genome browser. You learn how to create CNT and WIG files and import them into the genome browser.

SNP filtering

SNP QUALITY CONTROL: FILTERING SNPS BEFORE ANALYSIS

This tutorial shows you how to filter "poor quality" SNPs from your dataset before running analysis. You learn how to calculate marker statistics, isolate a list of "poor quality" SNPs and remove them from your dataset according to your quality control criteria.
Gender Check

CNV QUALITY ASSURANCE: LOG RATIO GENDER CHECK

This tutorial shows you how to check concordance between reported gender and imputed gender. You learn how to impute gender based on both X and Y chromosome log ratios, check for mismatches with reported gender and visualize data to assess outliers and possible causes of discrepancies.

ILLUMINA MARKER MAP EXPORT

This tutorial shows you how to create an Illumina marker map. You learn how to use Illumina’s BeadStudio software to export a marker map containing the SNPs, Chromosome and Physical Position pertaining your particular dataset under study.

Genetic Association & Predictive Analytics

GENETIC ASSOCIATION AND PREDICTIVE ANALYTICS WITH HELIXTREE

This recording is a complete overview demonstration of HelixTree Software as of version 5.3. You learn how to do everything from importing and processing data, performing various association methods, and building highly accurate predictive models.