Calculating odds ratio for single variable
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14 months ago
biobudhan ▴ 20

I am trying to understand what are the odds of a SNP being in intergenic, intronic, exonic, UTr3 or UTR5 regions. My data looks similar to this:

ID  chrom        pos      ref   alt homozygosity      heterozygosity      sampleMaf refSeq.siteType homo_ref        het  homo_alt       total.samples
snp1    chr4     123786114  A   G   0.0297               0.264               0.162        intronic      190 71  8   269
snp2    chr6    4014962         G   A   0.00743              0.149               0.0818      intergenic     227 40  2   269
snp3    chr4    6308762         T   C   0.0186               0.23                0.134        UTR3          202         62  5   269
snp4    chr4    98918764    C   T   0.138                0.435               0.355        exonic         115    117 37  269

I have the above information and I am not sure how to proceed.

oddsratio variant-annotation SNP • 323 views
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