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.
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