Diagnostic Plots for SNP quality assesment
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19 months ago
pixie@bioinfo ★ 1.5k

Hello, I have recently starting handling GBS data (around 115 samples). I have the filtered VCF files from two different runs. I wish to plot some SNP quality stats to compare the runs. I was specifically looking into this link: SNP quality assesment

I am interested in

  1. SNP depth or Genotype depth
  2. SNP observed heterozygosity
  3. Depth distributions per sample for all genotype calls and for the non-missing genotype calls
  4. Sample observed heterozygosity

Is there any R package which I could try ? Any other quality stats ? Thanks

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