This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Genetic Map file format: how to understand the combined_rate column and the genetic_map column ?

Hi guys,

The genotype imputation need human genetic map file, whose format is like(in chr1):

position COMBINED_rate(cM/Mb) Genetic_Map(cM)
55550 0 0
568322 0 0
568527 0 0
721290 2.685807669 0.410292036939447
723819 2.8222713027 0.417429561063975
723891 2.9813105581 0.417644215424158
728242 2.9806151254 0.430612871834774
729948 3.0780969498 0.435864105231133
740857 3.075133293 0.46941073432447

There are 3 columns, the first column is physical position united in bp, which is easy to understand. The second and third column is recombination rate(cM/Mb) and genetic position(cM, centiMorgan). I'm confused about the values in column 2 and 3.

Let's take the 4th row as an example. I know 721290 means the 721290th position on chr1. So what's the 2.68 and 0.41 represent for? I looked up some webpages and learned that "A centiMorgan is a unit of genetic distance that represents a 1% probability of recombination during meiosis." But I still cannot figure out the what's the meaning of 0.41/2.68 at position 721290.

Can anyone explain it to me? Thanks!

Tao

genetic map centimorgan
• 10,497 views • link
updated by 2649935201 • 2649935201 • written by Tao Tao

3 answers

Hi, Tao.

Let's take the 4th row as an example. 1. 721290 means the 721290th position on chr1 and also means 0.721290 Mb.

  1. To find 2nd column you need not numbers from 1st and 3d columns, but results of the subtractions: in the 4th row, it will be (0.41...-0)/(0.721290-0.568527) which gives us 2.685807669. So, in each row in column 1 and 3 you need to subtract numbers from the previous one to find the number from column 2.

Hope that it'll help you

Igor

• 0 views • link
written by archimyed • archimyed

For the first SNP on the rest of the chromosomes there is a rate(cM/Mb) > 0 when cM is 0. First chromosome is not good example. How is this calculated or it is inferred somehow. For instance this is first 5 on chromosome 2:

chr position COMBINED_rate(cM/Mb) Genetic_Map(cM)
2 12994 0.5043954585 0
2 15491 0.4706272937 0.0011751563523689
2 15672 0.4287316372 0.0012527567787021
2 15703 0.3838002191 0.0012646545854942
2 16111 0.3410386606 0.001403798359019

How do you get 0.5043954585?

• 0 views • link
written by bjwiley23 • bjwiley23

Hi, Tao There is a simple way to generate genetic map file. the 3d columns will be (position/1000000), and the 2nd columns will be [(next position - position)/1000000] Hope that it'll help you zuoquan

• 0 views • link
written by 2649935201 • 2649935201

Hi, Tao There is a simple way to generate genetic map file. the 3d columns will be (position/1000000), and the 2nd columns will be [(next position - position)/1000000] Hope that it'll help you zuoquan

• 0 views • link
written by 2649935201 • 2649935201

Log in to answer this question.

More posts like this
  • Convert Recombination txt file to Plink format
    written by nanodano • nanodano
    Hi everyone, I have a recombination map downloaded from the Broad Institute (https://alkesgroup.broadinstitute.org/Eagle/downloads/tables/) that looks like this: ``` chr position COMBINED_rate(cM/Mb) Genetic_Map(cM) 55550 0.0000000000 0.000000000000000 …