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Implement snpeff annotation, snp-df nb and process nbs #82

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merged 5 commits into from
Jul 26, 2023

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sanjaynagi
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This PR will resolve #80 #81 and #71.

  1. We introduce Snpeff for variant annotation. db is specified in the config.
  2. We implement a notebook, snp-dataframe, which converts vcf to dataframe and .xlsx
  3. We add a notebook, process-notebooks, which adds a cell tag to each nb, so that papermills injected parameters do not show up in the results-book.

@ChabbyTMD Please take a look when you can. I've also made some changes over the last day or two, adding whole amplicon variant calling #78 and a welcome message when starting the workflow #76 .

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Quite a great implementation of snpeff and the other features . I'll test them on my end and let you know if everything is all good.

@sanjaynagi sanjaynagi merged commit 6084211 into main Jul 26, 2023
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@sanjaynagi sanjaynagi deleted the snp-eff-and-snp-df-and-process-nbs-26-07-23 branch July 31, 2023 20:33
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Implement variant annotation
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