Question: Merlin ped file issue
gravatar for emyli
2.9 years ago by
emyli10 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 --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:

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 • 1.1k views
ADD COMMENTlink modified 2.3 years ago by bcvona0 • written 2.9 years ago by emyli10
gravatar for bcvona
2.3 years ago by
bcvona0 wrote:


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 2.3 years ago by bcvona0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 943 users visited in the last hour