Why parametric linkage analysis on Merlin gives zero "0" LOD score?

Question

[eDNAuRNA]

Hi all,

I am using Merlin for linkage analysis of large families. The SNP genotype file contains about 150K SNPs. I used Alohomora tool to get merlin input files. I can see negative, positive and zero LOD scores with I am trying single-point parametric linkage analysis with different models. But when I go for multi-point parametric linkage analysis with the same data, merlin gives the out put with zero LOD score on all markers of all chromosomes. I have tried many things but I am unable to trouble shoot it. An urgent help will be appreciated.

Thanks

[Ram]

Please read posts under https://biostars.org/t/how-to

This post is a question about a tool, not a tool-announcement post.

Answer 1

[Regina Phalange]

Hello! Although it's a very old problem, I have encountered the same issue and it was difficult to find relevant answers through search. Finally, I checked my PED file and found that there was an issue with the family relationships. Please double-check your phenotype and kinship relationships.