Unexprected Ensembl-vep results

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2.5 years ago

langzvi • 0

Hi.
I got a VCF from an individual that shows symptoms of a known disease with known mutations. I run it with Ensembl-vep, expecting to find some of those mutations in the results, yet, all the consequences in the results are "intergenic-variant".
The command I used was:

--cache --input_file sample.vcf

According to the VEP summary, the annotation source was:
Cache: /.vep/homo_sapiens/106_GRCh38; homo_sapiens_core_106_38 on ensembldb.ensembl.org

Any ideas why I got this results instead of the expected annotations? From your experience, could the Ensembl-vep result be wrong as a result of the command I used (the VCF file is ok)?
Thanks!

vcf mutation-detection ensembl-vep • 1.2k views

ADD COMMENT • link updated 2.5 years ago by GenoMax 148k • written 2.5 years ago by langzvi • 0

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maybe your VCF is not GRCh38?

ADD REPLY • link 2.5 years ago by JC 13k

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How can i know which is it?

ADD REPLY • link 2.5 years ago by langzvi • 0

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Look in the VCF file header to see if there is a record of genome build used.

ADD REPLY • link 2.5 years ago by GenoMax 148k

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According to the header, the reference was "human_g1k_v37". I read that it's a version of hg19. If it's so, than the reference I used might be the issue. Now I need to find how to download and use the hg19 instead of hg38. Thanks.