Geva does not make use of the genetic map file

[Luker121]

Hi,

I want to try the conversion by using a genetic map file with following command: ./geva_v1beta --vcf vcfile.vcf.gz --map ./geneticmap_file --out output

My genetic map file looks like this:

Chromosome  Position(bp)    Rate(cM/Mb) Map(cM)
chr1    1243674 0   0
chr1    1256937 0.116077705961259   0.145902363497827
chr1    1257119 0.232121801512549   0.291804726995654
chr1    1342929 0.926327090266299   1.24399151300423
chr1    1343070 1.03486331799687    1.38989387650206

But the output file does not contain the recombination rate and the genetic distance column. It has just 0's:

MarkerID Chromosome Position Label Alleles AlleleCount0 AlleleCount1 AlleleCountX GenotypeCount0 GenotypeCount1 GenotypeCount2 GenotypeCountX RecombRate GenDist
0 1 2209 . C,G 22 2 0 11 0 1 0 0.00000000 0.00000000
1 1 5109 . G,A 18 6 0 9 0 3 0 0.00000000 0.00000000
2 1 5263 . C,A 22 2 0 11 0 1 0 0.00000000 0.00000000
3 1 5891 . G,A 22 2 0 11 0 1 0 0.00000000 0.00000000
4 1 6032 . T,C 12 12 0 6 0 6 0 0.00000000 0.00000000

Can you imagine why this is? When running it with a fixed recombination rate (--rec) it works perfectly fine, it's just that the genetic map file does not work properly.