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Annotate hs37d5 genome calls using VEP

I have genome sequencing data in vcf format that I would like to annotate using VEP. The genomic variants were called against the hs37d5 reference genome, and I can't seem to find VEP cache files for this assembly. How can I annotate these variants using VEP?

vep annotation 1kgenomes hs37d5
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updated by jackplug350 • jackplug350 • written by igor • igor

Check for hg19, I am 100% sure you will find it via that name.

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written by ATpoint ATpoint

It is the same coordinate system with additional decoy sequences, you are good to go with using the hg19 VEP annotations. These decoys are intended to catch false alignments in case that somatic cells in fact have viral integrates which is not uncommon. It is the same reference genome though.

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written by ATpoint ATpoint

I always thought they were (at least for the major chromosomes) fully identical, hmm... This is based on checksum, I do not know, cannot contribute any further, sorry.

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written by ATpoint ATpoint

Hi Igor, were you able to find a solution?

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written by pattijane • pattijane

1 answer

Hi igor,

The VEP can annotate variants using a custom cache defined in GFF/GTF files supplied in the VEP query. More information can be found on the following documentation page: https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#gff

Best wishes

Ben Ensembl Helpdesk

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written by Ben Moore Ben Moore

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