Hi, I am using FBAT for association/linkage analyses with my NGS data. I have some data format problems and the corresponding person of that software does not reply (probably the software is too old). Does anyone have experience FBAT?
Here is my problem: I have my .ped file and when I load it and perform the normal "fbat" command everything seems to work (I got result tables). However, when I type "fbat -m" the software tells me "only bi-allelic markers are supported" and the test does not even start to run. I definately have no multiallelic markers in my .ped file. I also tried loading a .map file first and then the .ped file; the fbat -m test does not work either.
I thought the problem is my allele coding since I have large indels in my data set which are coded by long strings of integers. However, it does not seem that this is a problem.
Thanks for every hint!
Besides the notation problem of your larger indels, are you sure you have no large indels overlapping with a SNP? Because that would be a multiallelic site. I think for linkage analysis it's safe to remove indels from your analysis, at least that's the first thing that I would try in this case.
Thank you for that suggestion! I removed all indels. FBAT multimarker tests still give the error message "only bi-allelic markers are supported". I recognised that I have some double genetic positions within my dataset (if SNPs are located within short distance of 3 or 4 bases). I removed all those with double positions. I still get the same error message. I am wondering whether this error message is just the only one out and the error is something different. However, the single-marker test works.