[ensembl-dev] VEP - Reference contig not present

Hans Vasquez-Gross havasquezgross at ucdavis.edu
Fri Aug 22 19:41:33 BST 2014


Hi Will,

Thank you, that all makes sense to me.  We are doing an analysis on wheat,
but the cultivar is different then the assembly in Ensembl, which is why we
are seeing these result in the VCF.

For our project, we supplemented the Ensembl reference with a DeNovo
assembly of unmapped reads.  We didn't use any of the Ensembl core database
tools for this process.  However, I'd be interested to learn more about
creating our own VEP cache file from a custom annotation GTF and FASTA
file.  Maybe we should talk off list?  Thank you.

Cheers,
-Hans
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