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Summary report generator for first release of clockwork variants #17

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iqbal-lab opened this issue Feb 23, 2018 · 0 comments
Open

Summary report generator for first release of clockwork variants #17

iqbal-lab opened this issue Feb 23, 2018 · 0 comments

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@iqbal-lab
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iqbal-lab commented Feb 23, 2018 •
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  1. Stats on number of SNPs, indels etc (total number of SNPs, and indels at different sizes, and then number of SNPs, indels per sample)
  2. Stats on number of known/unknown AMR mutations
  3. Number of samples with a deleted/broken AMR gene
  4. Plot on fixed tree (split by country) (Phelim has a tree and methods)
  5. Lineage breakdown for each country
  6. Number of mixed samples per country
  7. Scatter Plot of number of hets per sample
  8. Plot across chromosome of SNP density summing across all samples
  9. Frequency distribution of SNPs
  10. Summary of Mykrobe results: counts of each AMR SNP/indel per country?
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