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For anyone that may be using SimWalk (v2.91) software, I would like to know if you have encountered similar behavior.
I have run mistyping analyses on each chromosome of a mammalian genome with the goal to create an output file that displays problematic genotypes within our pedigree. For about half of the chromosomes I do indeed see the output I want, and the results seem reasonable. For the other half, the output file is empty, with a log file stating that the run ended successfully. Additionally, the observed recombination distances between markers in the problematic runs are all listed as 0 (which is not reflective of the actual data). This is the only difference I see between runs that work and runs that do not. I've tried many different things, mainly involving messing with the parameters file, but have still not been able to correct this.
For people that have used this software, I am happy to clarify anything that I glossed over here.
Thanks!
I have run mistyping analyses on each chromosome of a mammalian genome with the goal to create an output file that displays problematic genotypes within our pedigree. For about half of the chromosomes I do indeed see the output I want, and the results seem reasonable. For the other half, the output file is empty, with a log file stating that the run ended successfully. Additionally, the observed recombination distances between markers in the problematic runs are all listed as 0 (which is not reflective of the actual data). This is the only difference I see between runs that work and runs that do not. I've tried many different things, mainly involving messing with the parameters file, but have still not been able to correct this.
For people that have used this software, I am happy to clarify anything that I glossed over here.
Thanks!