Question: calculating LD-tools to calculate D' in DNA sequencing data with unphrased genotype
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3.7 years ago by
ren.yingxue0 wrote:

Hi, I have a VCF file with a list of ~300 SNPs of interest from exome sequencing. I would like to calculate both D' and r2 for each pairwise comparison using my own sequencing data (as opposed to using HAPMAP/1000G). However, the genotypes in the VCF file are unphased. I have discovered that both VCFtools and Plink can calculate r2 from VCF files, but neither of them can calculate D' for unphased data. Does anyone have experience calculating D' from unphased sequencing data? Do you know of any tool that can perform the calculation? Many thanks!

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