Question: Why is VCFTools excluding so many SNPs in its Tajima D calculation?
1
gravatar for Ace
16 months ago by
Ace80
Ace80 wrote:

I used VCFTools to calculate Tajima's D for my population. When I started doing more specific analyses, I found that while VCFTools (via allele freq) recognized 22 SNPs in a certain gene, it was only including 5, total, into all the regions that fell into that area, producing many NA windows. Is this an outcome of certain parameters required for inclusion into its TajimaD testing?

ADD COMMENTlink modified 15 months ago by Biostar ♦♦ 20 • written 16 months ago by Ace80

Ive got no answer apart from try to use vcf-kit instead.

ADD REPLYlink written 16 months ago by Mark890
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