mira1

I have calculated individual inbreeding coefficients in PLINK software ( --het) and took the average of all individuals from a population to calculate inbreeding in the different populations. These coefficients are based on loss of heterozygosity (i.e. based on observed versus expected number of homozygous genotypes). Now, I have calulated observed and expected heterozygosity (Ho and He), also in PLINK software (--hardy), and for each population Ho is larger than He while in the table of individual inbreeding coefficients the number of observed homozygous genotypes is larger than the number of expected genotypes. So, this would mean that there are more heterozygous individuals than expected. How come? or do I interpreted the results in the wrong way? I also cannot find how these parameters are exactly measured and what's the difference between them. I hope someone has an answer. In addition, for both calculations I used a pruned dataset (--mind 0.1 --maf 0.05 --geno 0.1 --hwe 0.001 --indep-pairwise 100 25 0.2)

I made an IBS distance matrix using PLINK and would like to use this matrix to build a neighbor joining tree in 'Neighbor' of the PHYLIP package. When I read in the resulting matrix from PLINK in Neighbor and try to run then I get the following message: 'ERROR: diagonal element of row 1 of distance matrix is not zero' What goes wrong? Can I not directly use the PLINK output? How can I solve this problem? I'm not really familiar with these methods so I hope someone could help.

I am currently working on my master thesis and I have calculated some individual inbreeding coefficients and Fis per population. Can someone explain why Fis for a population is negative (e.g. -0.011) and individual inbreeding coefficients of that population are all positive / mean individual inbreeding coefficient of that population is positive (e.g. 0.242)? Fis values were calculated in FSTAT program. And individual inbreeding coefficients were calculated in PLINK software. (SNPs that had LD>0.1, MAF < 0.05 and more than 10% missed genotypes were excluded from the original dataset before analysis) I hope someone has an answer to my question. Thanks in advance!