hg38 for Gemini vcf database?

[bionewbie]

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.

[jennaj]

Hello @bionewbie

@bionewbie

Does anyone know whether there is a gemini for hg38?

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

@bionewbie

If there is not a gemini for hg38 (only hg19) what is the best alternative?

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

Best!