Ensembl 86 annotations with SnpEff for GRCh37

Question

[raghus606]

Hello Folks,

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.

Thank You

[WouterDeCoster]

To which genome did you align and call variants subsequently? Should be the same as you use for annotation, but based on this error I suspect it isn't.

[raghus606]

Yea that seems like the problem. We aligned using hs37d5 (build 37 with decoys) , the warning seems to indicate that the release 86 reference file is different to this, which is a little confusing since my assumption was that all build37s reference files should be the same atleast for the autosomal, X, Y and MT contigs.

[WouterDeCoster]

Well that explains it.

Answer 1

[Abdul Rafay Khan]

Go to http://ensembl.org/index.html and click View in archive site and select Ensembl 75: Feb 2014 (GRCh37.p13). It will take you to Ensembl 75.

Or go to http://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/

[WouterDeCoster]

Is that an answer to the problem?

[raghus606]

No, I was looking for a way to get ensembl release 86 for GRCh37 to work correctly with SNPEff.