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Linkage disequilibrium from multi-sample vcf file
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12 months ago
felipead66 • 30

I have a multi-sample vcf file annotated with snpeff.

I want to calculate the linkage disequilibrium.

I have 2 questions:

  1. I use vcftools, in particular ./vcftools --vcf input_vcf.vcf --geno-r2 --out output and it takes forever (it runs a week and keeps on). Is this OK?

  2. Is it appropriate to use the multi-sample vcf or should i calculate the ld for each vcf/sample?

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