Has anyone successfully managed to Annotate using a newer Ensembl annotation database with SNPEff ?
It seems the last prebuilt database for GrCh37 with SNPEff is 75. We followed the insturctions on SNPEff's website and built the database with ensembl release 86 (ftp://ftp.ensembl.org/pub/grch37/release-86/) and proceeded with the annotation.
However, the warnings seem to indicate that the coordinates are incorrect, particularly we have variants with : WARNING_REF_DOES_NOT_MATCH_GENOME.
Was curious if anyone has run into similar problems.