I am interested in calculating the integrated haplotype score (iHS) for SNPs surrounding a large candidate region of a particular human chromosome.
I have downloaded the latest phased haplotype data for the 1000 genomes data in addition to the map files: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20110521/
I have written a perl script to select out columns grouping all subjects belonging to a particular population together in an individual file (CEU, MEX, etc). I am interested in taking these data and for each population calculate the iHS.
There is a C script at the Pritchard group home page which allows for the calculation of iHS of SNP data: http://hgdp.uchicago.edu/Software/
However, the input for this requires genomic distance (in centimorgans) as one of the input columns for the map file. The most recent centimorgan data I can find for 1000genomes data is for Phase1 from 2008: ftp://ftp.hapmap.org/hapmap/recombination/2011-01_phaseII_B37/
Does anyone know if centimorgan position data has been estimated and if it is available for more recent 1000genomes SNP data?