Changes

=== Quality Control ===

=== Quality Control ===

You should apply standard quality control filters to the set of SNPs that you use as input to the imputation procedure. These filters are typically study specific but usually include checks for genotype completeness (markers with relatively high missingness rates are typically excluded), hardy weinberg equilibrium, duplicate concordance and sample heterozygosity. With older genotyping platforms, low frequency SNPs are often also excluded. Two good ways to verify that you have used appropriate quality control steps are to generate a Q-Q plot for your dataset and to calculate a genomic control parameter.

You should apply standard quality control filters to the set of SNPs that you use as input to the imputation procedure. These filters are typically study specific but usually include per marker checks for genotype completeness (markers with relatively high missingness rates are typically excluded), hardy weinberg equilibrium and duplicate concordance (markers with high discordance rates are excluded) and per sample checks for completeness and heterozygosity. With older genotyping platforms, low frequency SNPs are also often excluded. Two good ways to verify that you have used appropriate quality control steps are to generate a Q-Q plot for your dataset and to calculate a genomic control parameter.

=== Reference Haplotypes ===

=== Reference Haplotypes ===