Compute Genetic Map

Question

[Pierre]

Dear all,

I would like to get the position in cM for a set of SNPs (SNPs from 1000Genomes Project). What I have is:

• list of SNPs with their physical position
• Genotype (or infered genotype) for each SNP for around 50 individuals

Some of these snps (around 25%) are among the HapMap II SNPs used to compute the genetic map available on HapMap webpage (http://ftp.hapmap.org/recombination/2008-03_rel22_B36/rates). But is it enough information to calculate the cM position for 1000genomes SNPs from HapMap II genetic map?

What do you suggest?

Thanks for your help.

Yours truly Pierre

[Zach Stednick]

FYI, I could not get that link to work but has now been changed to: ftp://ftp.hapmap.org/hapmap/recombination/2008-03_rel22_B36/rates/

Answer 1

[Pierre Lindenbaum]

I hope I understand your question: The UCSC genome database contains the position in both base index and cM for the STS. e.g.:

~> mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg18 -e 'select name,chrom,chromStart,chromEnd,genethonPos from stsMap where genethonPos!=0 limit 2\G'
*************************** 1. row ***************************
       name: AFM280WE5
      chrom: chr1
 chromStart: 3574721
   chromEnd: 3575045
genethonPos: 6.2
*************************** 2. row ***************************
       name: AFM344WE9
      chrom: chr1
 chromStart: 4358261
   chromEnd: 4358654
genethonPos: 11.1

So you can use this STS map as a 'reference' to map your collection of SNP from bp to cM.

Answer 2

[Steve Buyske]

The Rutgers Map has an interpolate feature that can be used for any SNP not too near the telomeres or centromere.

http://compgen.rutgers.edu/RutgersMap/InterpolateMap.aspx

Answer 3

[Pierre]

Hey Pierre,

thanks for your answer! I already got the genetic map provided by USCS database with STS markers. But my issue remains the same: the density of markers of the available genetic maps (the USCS one or HapMap II one) is much lower than the density of my SNP set. For example I have 4054 SNPs between the 2 STS markers above (in your comment).

Therefore I don't know how to attribute to each SNPs of my set a position in cM without doing a very important approximation.

Anyway, what do you suggest? To use a rule of three approach to attribute a cM position to my collection's SNPs?

Thanks for your advice! Pierre

[Yuri]

I doubt you can get better resolution since centimorgan is experimental unit for recombination frequency. It does not correlate well with base pairs, which depends on genomic position. In human it approximately 1 Mbp in average.

[Pierre]

ok Thanks. I finally adopted this solution which provides satisfying results!

[Zach Stednick]

What solution did you eventually adopt?

[ice4prince]

Hi Pierre,

How did you solve it finally? I just have the same problem with you.