Cheng Chen

Hi Pasi, I am using LEP-MAP3 to construct a genetic map for a Vitis (232 samples, with 500Mb genome size, 19 chromosomes) interspecific population. The resulting map appears unusually long in genetic distance (cM), and I suspect this may be due to the very large number of SNPs I am using (about 320,000). I noticed that the example vcf file only contains ~ 2000 SNPs. Could you please advise on recommended approaches for filtering SNPs to retain only the most informative markers for accurate mapping?...

Hi Pasi, Thank you for your reply. I’ve tried running the process again, but the results were similar. I noticed that the OrderMasker output for Chromosome 1 is significantly larger than for the others (98 Mb vs. ~1 kb). I checked the ParentCall results, and the SNPs appear to be normally distributed across different chromosomes — is that correct? It seems like the linkage groups might not have been properly assigned to their respective chromosomes. When I reviewed the SeparateChromosomes2 map file,...

Hi Pasi, I am using LEP-MAP3 orderMarkers2 to construct a genetic map. The population I'm working with is derived froman interspecific cross between two species within Vitis. However, I noticed that the marker positions for one parent are completely missing in some chromosome of the output files. I'm not very familiar with genetics, so I would really appreciate your help in understanding where the issue might be. #java OrderMarkers2 map=map5_js.txt data=data_f.call chromosome=14 randSeed=-2790967626678564236...