Pasi Rastas

You could also see if there are individuals with too many recombinations. Typically problematic individuals show up as this. OrderMarkers2 output the individual recombinations (to error stream). Summing over all LGs would show if there are such outliers...

To add, It seems the LG12 problem and the problems in the first map are similar. That is, typically map end is duplicated for some reason. This could be because some individual(s) are not correct for some reason. Did you check the IBD values between parents and offspring? This could indicate individuals casing the end to be twice in the map. The LMPlot module (from output from OrderMarkers2, possible without outputPhasedData=2) can also indicate individuals causing these problems... Cheers, Pasi

To add, It seems the LG12 problem and the problems in the first map are similar. That is, tyically map end is duplicated for some reason. This could be because some individual(s) are not correct for some reason. Did you check the IBD values between parents and offspring? This could indicate individuals casing the end to be twice in the map. The LMPlot module (from output from OrderMarkers2, possible without outputPhasedData=2) can also indicate individuals causing these problems... Cheers, Pasi

To add, It seems the LG12 problem and the problems in the first map are similar. That is, tyically map end is duplicated for some reason. This could be because some individual(s) are not correct for some reason. Did you check the IBD values between parents and offspring? This could indicate individuals casing the end to be twice in the map. The LMPlot module can also indicate individuals causing these problems... Cheers, Pasi

Dear Achyut Duwadi, Indeed, the second map looks much better. The LG12 in the second map seems strange, running OrderMarkers2 again there might help there. If not, removing map positions 0-30cM might fix this. Are the linkage group numbers corresponding to each other. The yaxis span different ranges, so I am not sure. Be sure not to remove too many markers due to too large sizeLimit (=209). Some of the smaller linkage groups could be from the regions without markers. I am seeing the centromeres in...

Dear Achyut Duwadi, Thank you for your question. In this case, you could just edit the mapM.txt file manually to join LG2 and LG11 together. I typically run SeparateChromosomes2 several times, starting with small lodLimit and increasing it and give the map parameter the result of the previous round on SeparateChromosomes2, e.g. java SeparateChromosomes2 ... distortionLod=1 lodLimit=8 >map8.txt java SeparateChromosomes2 ... distortionLod=1 lodLimit=9 map=map8.txt >map9.txt ... For the informativeMask...

Dear Molly, Sorry, the IBD module is not fully documented. I have made it to ease such analysis for myself, and published it for others as well if they find it useful. It finds a maximum likelihood probabilities Px for each pair of individuals for IBD sharing of x alleles (x=0..2). It outputs (P2+0.5*P1) as column 3, and the individual Px values. I assume your data is from a diploid species. Then the IBD between parent and offspring should be 0.5 if the parents are unrelated. With related parents,...

Dear Molly, Sorry, the IBD module is not fully documented. I have made it to ease such analysis for myself, and published it for others as well if they find it useful. It finds a maximum likelihood probabilities Px for each pair of individuals for IBD sharing of x alleles (x=0..2). It outputs (0.5*P2+P1) as column 3, and the individual Px values. I assume your data is from a diploid species. Then the IBD between parent and offspring should be 0.5 if the parents are unrelated. With related parents,...