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Revision as of 07:11, 8 April 2011
, 07:11, 8 April 2011→Your Own Data
The latest reference panel generated by the 1000 Genomes project uses NCBI Build 37 (HG 19). Make sure that your data is on Build 37, otherwise lift your data over.
The latest reference panel generated by the 1000 Genomes project uses NCBI Build 37 (HG 19). Make sure that your data is on Build 37, otherwise lift your data over.
=== 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 and duplicate concordance. 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.
=== Reference Haplotypes ===
=== Reference Haplotypes ===
