Created:
March 27, 2008

User Level:
Beginner

Products:
SVS


SNP QUALITY CONTROL: FILTERING SNPS BEFORE ANALYSIS

Quality control is an important step in any analysis, and there are workflows available in the SNP & Variation Suite (SVS) to automate these functions. For the following tutorial, we will be using call rate and minor allele frequency, but the same principals could be applied to other standards, such as Hardy-Weinberg Equilibrium, concordance measures, etc. Essentially, we will isolate a list of markers that do not meet specific criteria and then filter them from further analysis.

Overview:

  1. 1. Calculate marker statistics
  2. 2. Isolate data of interest
  3. 3. Deactivate columns by row labels


REQUIREMENTS

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

Prerequisite Knowledge:
Basic SVS functionality