Question: Merlin ped file issue
0
gravatar for emyli
2.1 years ago by
emyli0
emyli0 wrote:

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.

merlin linkage • 802 views
ADD COMMENTlink modified 17 months ago by bcvona0 • written 2.1 years ago by emyli0
0
gravatar for bcvona
17 months ago by
bcvona0
bcvona0 wrote:

Hi,

Have you by chance had any luck in this? I am also seeing the exact same problem. Thank you very much in advance!

ADD COMMENTlink written 17 months ago by bcvona0
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