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, 09:35, 30 May 2012
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| 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: [http://www.sph.umich.edu/csg/cfuchsb/metab_order_changed.txt List of Metabochip SNPs Whose Order Changes With Build] | | 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: [http://www.sph.umich.edu/csg/cfuchsb/metab_order_changed.txt List of Metabochip SNPs Whose Order Changes With Build] |
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− | Note: For the most recent reference panel in VCF format GWAS SNPs have to be in the chr:pos format e.g. 1:1000 (NOT rsxxxxx) | + | 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, if you are using rsXXX identifiers you have to set the --rs flag |
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| === Quality Control === | | === Quality Control === |