This folder contains a build GRCh37 genetic map.

The map was generated by lifting the HapMap Phase II genetic map from build 35 to GRCh37. The original map was generated using LDhat as described in the 2007 HapMap paper (Nature, 18th Sept 2007). The conversion from b35 to GRCh37 was achieved using the UCSC liftOver tool.

Once the liftOver was completed, the map was inspected for regions in which the genome assembly had be rearranged. Such rearrangements result in a dip in the lifted genetic map (i.e. a negative recombination rate). These regions were removed by setting the recombination to zero within, and for 50 SNPs either side of, such regions. These regions are fairly rare, and this method removed a total of 2013 SNPs from the following chromosomes.

chr1: 224 SNPs chr2: 209 SNPs chr3: 104 SNPs chr4: 103 SNPs chr7: 547 SNPs chr9: 292 SNPs chr10: 101 SNPs chr13: 208 SNPs chr15: 101 SNPs chrX: 124 SNPs.

All other chromosomes did not have any SNPs removed by this method.

Adam Auton 08/12/2010