Question: Calculating Tajima's D from vcf data using bed files
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gravatar for spiral01
21 months ago by
spiral01100
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 • 1.5k views
ADD COMMENTlink modified 11 months ago by Gabriel30 • written 21 months ago by spiral01100
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gravatar for Gabriel
11 months ago by
Gabriel30
Gabriel30 wrote:

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

ADD COMMENTlink written 11 months ago by Gabriel30
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