ANNOVAR alternative

[erike]

Hello, I’m a beginner who is working on a class project to identify and count polymorphisms between three datasets. I’m using the usegalaxy.eu server. So far the workflow I’ve come up with will use the FreeBayes tool to identify polymorphic sites and returns results in vcf format. I’ve based this workflow on some examples that I’ve found online and at this point the next step uses the ANNOVAR tool to annotate the various polymorphisms in the vcf file. However ANNOVAR doesn’t seem to be available on the galaxy server. I’ve looked for an alternative tool but I’m not exactly sure if there is one and if there is which tool should I use.

Best,
Erik E

[wm75]

Hi and welcome,
the suggested alternative is to combine SnpEff and GEMINI as ilustrated in these tutorials:

• https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/exome-seq/tutorial.html
• https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/somatic-variants/tutorial.html

BTW, the SnpEff eff tool is hard to find in the EU server tools bar due to a search functionality issue so here’s a direct link: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1

Best,
Wolfgang