550
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchMinimac: 1000 Genomes Imputation Cookbook (view source)
Revision as of 22:52, 10 February 2011
, 22:52, 10 February 2011no edit summary
== Quality Filtering ==
== Quality Filtering ==
For 1000 Genome SNPs, we currently recommend that any markers with estimated r<sup>2</sup> of <0.5 should be treated with caution. This is a bit more conservative than the threshold of 0.3 we recommend for HapMap; but 1000 Genome SNP genotypes are also (as of June 2010) of lower quality.
For 1000 Genome SNPs, we currently recommend that any markers with estimated r<sup>2</sup> of <0.5 should be treated with caution. This is a bit more conservative than the threshold of 0.3 we recommend for HapMap; but 1000 Genome SNP genotypes are also of lower quality. Be aware that imputation quality statistics are not directly comparable between different imputation programs (MaCH/minimac vs. Impute vs. Beagle etc.).
== Questions and Comments ==
== Questions and Comments ==
Please contact [mailto:goncalo@umich.edu Goncalo Abecasis] or [mailto:cfuchsb@umich.edu Christian Fuchsberger (minimac)] or [mailto:yunli@med.unc.edu Yun Li (MaCH)].
Please contact [mailto:goncalo@umich.edu Goncalo Abecasis] or [mailto:cfuchsb@umich.edu Christian Fuchsberger (minimac)] or [mailto:yunli@med.unc.edu Yun Li (MaCH)].
