Ensembl 86 annotations with SnpEff for GRCh37
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4.3 years ago
raghus606 ▴ 10

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

Variant Annotation • 1.3k views
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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.

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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.

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Well that explains it.

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4.3 years ago

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/

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Is that an answer to the problem?

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

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