Question: Calculating Tajima's D from vcf data using bed files
gravatar for spiral01
3.0 years ago by
spiral01100 wrote:

I need to calculate Tajima's D for vcf data, using a bed file to indicate the windows in which I want to calculate the statistic. I tried to use vcftools like so:

vcftools --gzvcf file.vcf.gz --bed file.bed --TajimaD 500 --stdout > output.txt

However vcftools requires that you indicate the size of the windows for which you wish to calculate the statistic (the 500 above). As such it ends up calculating Tajima's D for each scrolling window, instead of for each of the windows stipulated in my bed file.

Is there anyway to circumvent this, or any tool that is better suited to this task?

snp • 2.2k views
ADD COMMENTlink modified 2.2 years ago by Gabriel40 • written 3.0 years ago by spiral01100
gravatar for Gabriel
2.2 years ago by
Gabriel40 wrote:

Hi @spiral01, I am with the same issue here. Did you find a way to do it? Thanks! Gabriel

ADD COMMENTlink written 2.2 years ago by Gabriel40
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