hg38 for Gemini vcf database?

Hello. Two questions

  1. Does anyone know whether there is a gemini for hg38?
  2. If there is not a gemini for hg38 (only hg19) what is the best alternative?

Thank you.

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Hello @bionewbie

The Galaxy wrapped version of Gemini works with the hg19 genome. There are technical reasons why hg38 is not supported.

Quote from the tool form, as hosted at https://usegalaxy.eu: Gemini load

Only build 37 (aka hg19) of the human genome is supported.

GTN Tutorial that covers an example usage: https://galaxyproject.github.io/training-material/topics/variant-analysis/tutorials/exome-seq/tutorial.html

Gemini has unique functionality. Annotation and parsing tools are all one package. But there are many other tools to annotate/parse VCF datasets. Please see this prior Q&A for some tips: GEMINI load alternatives


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