Entering edit mode
6.6 years ago
qwzhang0601 ▴ 80
According to the document of vcftools "--site-pi Measures nucleotide divergency on a per-site basis". But does anyone tell me the exact formula to calculate the --site-pi given genotype data from one population?
I think the same question is asked here, just in case it will be of use: ""If useful, you can inspect the source code for the calculation. It's in the function 'output_windowed_nucleotide_diversity' in vcf_file_output.cpp"" https://sourceforge.net/p/vcftools/bugs/42/