Question: Linkage disequilibrium from multi-sample vcf file
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gravatar for felipead66
3 months ago by
felipead6630
felipead6630 wrote:

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?

ld vcftools snpeff vcf • 160 views
ADD COMMENTlink modified 3 months ago by RamRS24k • written 3 months ago by felipead6630
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