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Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
https://www.ensembl.org/vep
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No HGVS for Structural Variants #1222

Open Addy81 opened 2 years ago

Addy81 commented 2 years ago

Hello,

I was running VEP (v105) on some CNV data and was wondering if it is meant to output HGVS notation for the CNVs or not?

The fields are empty so making sure I haven't run it wrongly or missing anything.

My command:

docker run -v /home/dnanexus:/opt/vep/.vep b478f679ac19 ./vep -i /opt/vep/.vep/CEN35CNV2-CEN-F-EGG5_segments_temp.vcf -o /opt/vep/.vep/CEN35CNV2-CEN-F-EGG5_segments_temp_annotated.vcf.gz --vcf --cache --refseq --exclude_predicted --symbol --hgvs --hgvsg --check_existing --variant_class --numbers --format vcf --offline --exclude_null_alleles --assembly GRCh37 --fields Allele,SYMBOL,HGNC_ID,VARIANT_CLASS,Consequence,IMPACT,EXON,INTRON,Feature,HGVSc,HGVSp,HGVS_OFFSET,Existing_variation,STRAND,HGVSg --buffer_size 100 --fork 16 --no_stats --compress_output bgzip --shift_3prime 1

Example output I get:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  CEN35CNV2-CEN-F-EGG5
X   32827580    CNV_X_32827580_32841534 N   <DUP>   452.63  .   END=32841534;CSQ=duplication|DMD||duplication|splice_polypyrimidine_tract_variant&coding_sequence_variant&intron_variant&feature_elongation|LOW|5-7/79|4-7/78|NM_000109.4|||||-1|,duplication|DMD||duplication|splice_polypyrimidine_tract_variant&coding_sequence_variant&intron_variant&feature_elongation|LOW|5-7/79|4-7/78|NM_004006.3|||||-1|,duplication|DMD||duplication|splice_polypyrimidine_tract_variant&coding_sequence_variant&intron_variant&feature_elongation|LOW|5-7/79|4-7/78|NM_004009.3|||||-1|,duplication|DMD||duplication|splice_polypyrimidine_tract_variant&coding_sequence_variant&5_prime_UTR_variant&intron_variant&feature_elongation|LOW|5-7/79|4-7/78|NM_004010.3|||||-1|    GT:CN:NP:QA:QS:QSE:QSS  ./.:3:3:183:453:188:253

Any input would be greatly appreciated.

Many thanks,

Adriana :)

nakib103 commented 2 years ago

Hi @Addy81

Thank you for your query. We don't actually support HGVS for SV currently.

Hope that answers your query.

Best regards, Nakib

Addy81 commented 2 years ago

Thanks for the response @nakib103 !

Is it in your roadmap to support them in the future?

Many thanks, Adriana :)

nakib103 commented 2 years ago

Yes, we do have plan to support them in the future. I cannot comment on the exact timeline right now, but we will let you know once the feature is available.

Best regards, Nakib

davmlaw commented 6 months ago

Hi, could I suggest renaming this issue to something like "No HGVS for symbolic alts" (or Structural Variants) etc?

Was trying to find it, and it wasn't obvious this was the issue. Thanks