Pasi Rastas

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,...

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*P1+P2) 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 is 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*P1+P2) 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, Thank you for your question! Indeed, IBD does assume marker independence. Typically you are dealing with family data when doing linkage mapping, so I don't know if LD pruning is needed or proper here. Normally I have chosen a small random subset of markers for IBD module to verify the family structure, about 500-5000 markers has been enough, evenly over the genome. Maybe a limit on the physical distance between included markers could be the best, e.g. min distance of 1Mb between used...

Dear Ana, Thank you for your question. Can you share the number of marker in each linkage group? Typically you have several small groups which can be ignored. Below is the unix command to obtain this: sort map.txt|uniq -c|sort -n You hope to have the expected number of large groups and several much smaller ones. You seem to remove groups smaller than 15 with sizeLimit. It is very rare that you have to filter VCF files, typically Lep-MAP3 can do required filtering. For more aggressive segregation...

Dear Ana, Thank you for your question. Can you share the number of marker in each linkage group? Typically you have several small groups which can be ignored. Below is the unix command to obtain this: sort map.txt|uniq -c|sort -n You wold preferably have expected number of large groups and several much smaller ones. You seem to remove groups smaller than 15 with sizeLimit. It is very rare that you have to filter VCF files, typically Lep-MAP3 can do required filtering. For more aggressive segregation...