24 months ago by
Check the reference genome the FreeBayes data was generated against versus those in IGV/UCSC. Are these a match (exactly, including the build and chromosome identifiers)?
A mismatch is almost always the root of the problem for cases like this. If you want to share a snippet of the Galaxy VCF (header and first few lines) and the assigned metadata (database, datatype), plus the name of the build (database) at IGV and UCSC, this can probably be visually determined here.
Github gist is a good way to share text, or simply past the content into a comment reply.
Thanks, Jen, Galaxy team