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Quality Control Overview

7.1 Quality Control Overview

To ensure your data is of the highest quality, SVS provides a variety of features that not only help you assess the quality of your data, but remedy any problems as well.

The features in the software available for quality control are as follows:

Allele and Genotype Frequencies/Counts
Calculate the allele frequencies for both the major and minor alleles and allele and genotype counts for each marker in your dataset.

Call Rates
Calculate the fraction of called genotypes for each marker or sample.

Hardy-Weinberg Equilibrium P-Value
Determine how closely respective genotypes in your dataset approximate a state of Hardy-Weinberg Equilibrium (HWE) by calculating HWE p-values.

Fisher’s Exact Test for HWE P-Value
Determine how closely respective genotypes in your dataset approximate a state of Hardy-Weinberg Equilibrium (HWE) by calculating Fisher’s Exact Test for HWE p-values.

Signed HWE Correlation R
Determine how closely respective genotypes in your dataset approximate a state of Hardy-Weinberg Equilibrium (HWE) by calculating HWE correlation R values.

Hardy-Weinberg Thw P-value
Determine if genotypes for samples violate population-based transmission Hardy-Weinberg principles.

PBAT Family-Based QC Measures
Determine if genotypes violate PBAT family-based quality control measures, including Mendelian errors.

Genotype Principal Component Analysis
Adjust for population stratification on genotypic markers.

Numeric Principal Component Analysis
Adjust for batch effects or population stratification on log2 ratio data or other numeric data.

Genotype Gender Check
Verify the reported gender matches average X and Y chromosome intensities.

SNP Concordance
Calculate various concordance rates for all SNPs for a given set of samples.

Filtering Markers
Exclude data out of HWE, with a minor allele frequency or call rate below a user-specified threshold, or does not meet other quality control thresholds.