So my partner is struggling with getting the MORGAN v3.4 (PANGAEA program) parametric linkage to generate appropriate results, there are absurd LOD scores even for the "dummy" data (where they input data that both was and wasn't supposed to give them a suggestive or significant LOD score so they could test that the script was structured correctly and going to give appropriate results). They're trying to optimize both dominant and recessive linkage models, and based on the allele frequencies and penetrances they're inputting they should be getting significant LOD scores but they haven't gotten anything higher than a LOD of 1.2.
Here's the specifics, if anyone would be willing to shed some light on what may or may not be going wrong, we'd be super appreciative. Nobody in their lab or department has used MORGAN before so this is all very trial by error with no supervision.
https://drive.google.com/file/d/1eaS32JC9jwnI4BmE7hDDfmVG0Pftf7yr/view?usp=drivesdk
I usually recommend to start by playing with the example files distributed with the software. Are you getting the expected results with that? Another good option would be to share the pedigree and marker files as well, since the parameter file alone doesn't give much information.
This is a message from my partner:
Here are the example ped and marker files I am using for the parameter (par) file. These files closely simulate the data I am using, and I am using these files currently to run the analysis quickly while I tweak the parameters. I am assuming the penetrance values in the par file are what I use to alter mode of inheritance (from dominant to recessive). When age is added, changing the penetrance values does not change the LOD scores at all. However, with age removed, the penetrance values seem to then work (although significant linkage is still not found).
Thanks for any and all help!
https://drive.google.com/file/d/1Tj0kHFq9owtgAqzyLLtGer0TC6qzDnE5/view?usp=sharing
https://drive.google.com/file/d/1njjZnR01UCOMsof0AF1kgbmYk8jq_h4j/view?usp=sharing