CNV QUALITY ASSURANCE: LOG RATIO GENDER CHECK

An important quality control step for any genetic analysis is to verify your samples' reported genders match those imputed using their genetic data. This tutorial will help you assess gender concordance based on log ratios (LogRs) of the X and Y chromosomes.

NOTE: This tutorial assumes you have already prepared an uncorrected LogR DSF file. For help on this procedure, see Step 1 of the Whole Genome Copy Number Association Tutorial.

NOTE: The steps outlined in this tutorial are consistent with options in SVS v6.4 or later.

Overview:

1. 1. Import uncorrected LogRs for X and Y chromosomes (if available)
2. 2. Determine the appropriate LogR mean threshold to impute gender
3. 3. Impute gender based on LogR mean threshold
4. 4. Check concordance between reported gender and imputed gender
5. 5. Visualize data to assess gender deviations

REQUIREMENTS

To complete this tutorial, you will need the following software and files:

• HelixTree
• Copy Number Analysis Module
• SNP 6 HapMap LogR DSF (2GB)
• HapMap Phenotype Data CSV (10KB)

Prerequisite Knowledge:
Intermediate SVS functionality