About genetic position: two decimal places

[Qiuming1986]

Dear hardingnj,

I am a beginner. I know the software is very robust to detect selective sweep, especially with genetic positions in the input file. Now I have a ~100,000,000 SNPs file from whole genome sequence, however the genetic positions of only 50,000 SNPs have been identified by previous studies, moreover the genetic positions are accurate to two decimal places in my organism. The part of genetic positions is as follows:

SNP Chrom Position (pb) Position (cM)

 1  M1_42269    1H  42269   0.00
 2  M1_52020    1H  52020   0.09
 3  M1_51926    1H  51926   0.24
 4  M1_263510   1H  263510  0.24
 5  M1_289719   1H  289719  0.35
 6  M1_290049   1H  290049  0.35
 7  M1_563860   1H  563860  0.84
 8  M1_938228   1H  938228  0.84
 9  M1_945239   1H  945239  0.84
 10 M1_945329   1H  945329  0.84
 11 M1_1148945  1H  1148945 0.84
 12 M1_1184919  1H  1184919 0.84
 13 M1_1249406  1H  1249406 1.08
 14 M1_1512878  1H  1512878 1.26
 15 M1_1558406  1H  1558406 1.40
 16 M1_1328193  1H  1328193 1.49
 17 M1_2205078  1H  2205078 1.49
 18 M1_1277910  1H  1277910 1.68
 19 M1_1277969  1H  1277969 1.68
 20 M1_1312698  1H  1312698 1.74

my question are whether the genetic positions with the accuracy of two decimal places are suitable for this software, and how to get the genetic positions of the remaining SNPs of not knowing.

Thank you!

[hardingnj]

You will need more precise genetic map, each SNP should be a unique value. I think you could do two things:

• Use the genomic position as a proxy for the genetic_position (cM)
• Or estimate genetic position based on some function of approximate genetic position and genomic co-ordinates.