Question: Genetic Map in HapMap based on which population?
0
gravatar for GabrielMontenegro
3.5 years ago by
United Kingdom
GabrielMontenegro400 wrote:

I need to get the genetic map position for some SNPs so I downloaded the HapMap genetic map file provided here: http://hapmap.ncbi.nlm.nih.gov/downloads/recombination/

However I couldn't find any information regarding on which population this genetic map was based on. The README file only points to the 2007 HapMap Nature paper but I couldn't find any information there.

Thank you!

J

Ps. I also found a genetic map using 1k genomes Phase 3 based and all populations. Is 1kG more reliable than the HapMap genetic map?

 

recombination snps • 1.9k views
ADD COMMENTlink modified 3.5 years ago by Zev.Kronenberg11k • written 3.5 years ago by GabrielMontenegro400
2
gravatar for Zev.Kronenberg
3.5 years ago by
United States
Zev.Kronenberg11k wrote:
In the README:
00README.txt


Both recombination rates and hotspots were estimated separately for each HapMap analysis panel (YRI, CEU, CHB+JPT).  Recombination rates were averaged across populations and p-values for hotspots were combined such that a hotspot requires that two of the three populations show some evidence of a hotspot (p<0.05) and at least one population showed stronger evidence for a hotspot (p<0.01). Hotspot centres were estimated at those locations where distinct recombination rate estimate peaks (with at least a factor of two separation between peaks) occurred, within the low p-value intervals.  The width of the hotspot represents the region where the estimated rate is within a factor of two of the maximum. 
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Zev.Kronenberg11k
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