VEP: "Given ref" field is empty when a ref. allele was in VCF input
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Entering edit mode
4 weeks ago
rebeliscu ▴ 30

Hi there,

I'm running VEP using the following command:

ref="GRCh38.primary_assembly.genome.fa"
vep="/opt/vep_ensembl/ensembl-vep/vep"
for ea in *Somatic.hc.vcf
  do $vep -i $ea -o vep/"$(echo $ea | sed s/.vcf//)"_VEP.txt \
  --cache --dir_cache "/home/shared/vep_cache/" --assembly GRCh38 \
  --merged --fasta $ref --hgvs --hgvsg --symbol --pick --tab --fork 1 \
  --offline
done;

In some cases I get a blank entry for "given ref", e.g.:

head(temp)
   #Uploaded_variation      Location Allele Gene Feature Feature_type        Consequence cDNA_position CDS_position
1:   chr2_11077037_C/T chr2:11077037      T    -       -            - intergenic_variant             -            -
2:   chr2_90272360_T/A chr2:90272360      A    -       -            - intergenic_variant             -            -
3:   chr2_90272610_C/A chr2:90272610      A    -       -            - intergenic_variant             -            -
4:   chr2_90281038_C/G chr2:90281038      G    -       -            - intergenic_variant             -            -
5:   chr2_91477060_T/A chr2:91477060      A    -       -            - intergenic_variant             -            -
6:   chr2_91544770_T/C chr2:91544770      C    -       -            - intergenic_variant             -            -
   Protein_position Amino_acids Codons Existing_variation   IMPACT DISTANCE STRAND FLAGS SYMBOL SYMBOL_SOURCE HGNC_ID
1:                -           -      -                  - MODIFIER        -      -     -      -             -       -
2:                -           -      -                  - MODIFIER        -      -     -      -             -       -
3:                -           -      -                  - MODIFIER        -      -     -      -             -       -
4:                -           -      -                  - MODIFIER        -      -     -      -             -       -
5:                -           -      -                  - MODIFIER        -      -     -      -             -       -
6:                -           -      -                  - MODIFIER        -      -     -      -             -       -
   REFSEQ_MATCH SOURCE REFSEQ_OFFSET GIVEN_REF USED_REF BAM_EDIT HGVSc HGVSp HGVS_OFFSET              HGVSg
1:            -      -             -         -        -        -     -     -           - chr2:g.11077037C>T
2:            -      -             -         -        -        -     -     -           - chr2:g.90272360T>A
3:            -      -             -         -        -        -     -     -           - chr2:g.90272610C>A

Based on the "uploaded variation" field, it is clear that I am providing a ref. allele. Why is VEP not using this as the reference?

Thanks in advance.

WXS VCF VEP • 79 views
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