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Minimac: 1000 Genomes Imputation Cookbook

5 bytes removed, 21:44, 27 August 2012
Your Own Data
If you are planning to use imputation with the MetaboChip, you might find a list of SNPs whose order varies between NCBI genome build 36 and 37 convenient. Here it is: [ List of Metabochip SNPs Whose Order Changes With Build]
Note: For the most recent reference panel in VCF format by default GWAS SNPs are expected to be in the chr:pos format e.g. 1:1000; otherwise, for GWAS SNPs in the rs..... format you have to set the --rs flag
=== Quality Control ===

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