I have whole genome sequence from Saccharomyces cerevisiae strains and I'm looking for their variations from refseq. The reads have been worked up to .vcf files using Varscan and also FreeBayes on the useGalaxy web interface. They view nicely in IGB. I'm stuck at how one gets an excel list of the collection of variants with annotations for snps (or indels, etc)? Any videos, tutorials, comments appreciated. Thank you.
Annotations can be associated with the tools Annovar, SnpEff, VCF-BEDintersect, and other tools such as Gemini.
VCF format can be transformed to tab-delimited format with the tool VCFtoTab-delimited then download to import into Excel.
Galaxy tutorials: https://galaxyproject.org/learn/
Thanks! Jen, Galaxy team