Changes

=== Reference Haplotypes ===

=== Reference Haplotypes ===

Reference haplotypes generated by the 1000 Genomes project and formatted so that they are ready for analysis are available from the [http://www.sph.umich.edu/csg/abecasis/MaCH/download/1000G-2010-03.html MaCH download page]. The most recent set of haplotypes were generated in March 2010 by combining genotype calls generated at the Broad, Sanger and the University of Michigan. In our hands, this March 2010 release is substantially better than previous 1000 Genome Project genotype call sets.

Reference haplotypes generated by the 1000 Genomes project and formatted so that they are ready for analysis are available from the [http://www.sph.umich.edu/csg/abecasis/MaCH/download/1000G-2010-06.html MaCH download page]. The most recent set of haplotypes were generated in June 2010 by combining genotype calls generated at the Broad, Sanger and the University of Michigan. In our hands, this June 2010 release is substantially better than previous 1000 Genome Project genotype call sets.

== Estimating Model Parameters ==

== Estimating Model Parameters ==

== Quality Filtering ==

== Quality Filtering ==

For 1000 Genome SNPs, we currently recommend that any markers with estimated r² 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 March 2010) of lower quality.

For 1000 Genome SNPs, we currently recommend that any markers with estimated r² 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.