Centimorgan Values For Snps In Dbsnp132 And Higher?

Question

[Avariant]

Hi all, 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?

[lh3]

This depends on the genetic map, which varies slightly between populations and there is no universal consensus which is better. You can find the genetic map from hapmap, oxford or decode.

[Avariant]

OK, thanks. Do you know where on the decode or hapmap site you can download the map, in table format?

Answer 1

[deanna.church]

You can find a variety of non-sequence based maps, including several linkage maps, here: ftp://ftp.ncbi.nih.gov/genomes/MapView/Homo_sapiens/non_sequence/