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How to calculate the density of alternative alleles as a ratio in a window of 10 kb

Hello all,

I want to calculate the alternative alleles density in 10 kb and then plot the ratio (0 to 1) of alternative alleles vs positions

something like this:

https://img.techpowerup.org/191021/1381fig3.jpg

There is --SNPdensity option in vcftools, but I didn't find any option to calculate the alternative alleles

Any suggestions? which tool would do that?

Thanks

snp
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written by Hann Hann

Th image you reference does not feature alternative alleles, to me it looks like it's displaying SNP density (as some sort of SNP/Non-SNP ratio?). For allele frequencies, you would rather expect discrete step like sections, depending on ploidy (for example three states [0] - [0.5] - [1] for heterozygotes)

What exactly did you have in mind? An average alternative allele frequency per window? This will hide the step like nature you will find between homozygous/heterozygous sections

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written by Carambakaracho Carambakaracho

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