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I ran the following command:

/VCF2Dis-master/bin/VCF2Dis -InPut input.vcf.gz -OutPut output.mat

Since I generated this matrix for which a dataset for which pairwise genetic distance values were already available, I compared the results of VCF2Dis to the available results. It seems like the results differ by a factor of 10. When I divide the result values of VCF2Dis by 10, the results match to the already available dataset. Can you please explain -

What happens to the sites with missing data in one sample of the two samples in a pair

What is L in your formula? Is it the complete genome or just the sites which are considered for calculating genetic distance

hi，
I use this methods "an Example of nj-tree with boostrap", but I just get a tree "Final_boostrap.tre" with bootstrap values in tree branch rather than in tree node finnally!
Final_boostrap_test.txt

Hello, I am trying to construct a tree using the VCF file obtained from merging with GATK and bcftools. After using the VCF2Dis command to generate a .mat file, but there are many '-nan' in the result. Can you give me some suggestions?

Is there any descriptions about time and memory cconsumption? It would be helpful when running the program in PBS ( Protable Batch System).