550
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchMinimac: 1000 Genomes Imputation Cookbook (view source)
Revision as of 21:44, 27 August 2012
, 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: [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]
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
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 ===
=== Quality Control ===
