Hi, I'm trying to conduct parametric linkage analysis using SNP data and merlin. I'm using the basic command used in the merlin tutorial:
merlin -d test.dat -p test.ped -m test.map --model parametric.model --step 3 --bits 26 --megabytes:2048
and am receiving LOD scores of 0 for every single marker. I have also tried the basic command for non-parametric linkage and an error informing me this was an uninformative family was received.
I cannot see any discrepancies between my input files (.ped, .dat, .map) and the examples supplied by merlin. I have tried applying mock affection statuses to see if this is the issue, to no avail. The only issue I have found is that the pedstats summary of my pedigree reads:
Generations
Average: 5.00 (5 to 5)
Distribution: 5 (100.0%), 0 (0.0%) and 1 (0.0%)
While this correctly finds 5 generations in my pedigree, the distribution is wrong. This leads me to believe the ped file is the issue, however I have used it successfully in other programs, including paramlink in R.
I would attach examples of my files but am new here and cannot see a way to do so. Any ideas as to what might be going on or what to try would be most appreciated.
