shift_3prime bug

[fzhbioinfo]

Describe the issue

We use '--shift_3prime 1' that causes the variant's ClinVar CLIN_SIG to be unannotated.

Additional information

web tools : https://grch37.ensembl.org/Tools/VEP
variant ：10 101606808 . G GCT . . .
CLIN_SIG : Pathogenic

with '--shift_3prime 1' : https://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Results?tl=7At9ktOQsUD7BJ2S-10666157
without '--shift_3prime 1' : https://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Results?tl=K7BSm1KlvYXOWQou-10666152

While running VEP with ClinVar as a custom file, the same issue will occur. We look forward to your solution to this issue.

[olaaustine]

Hi @fzhbioinfo,
Hope this meets you well?
Can you share your custom command?
I am able to recreate this issue depending on the command being used, so I need to verify your command.
Thank you
Ola

[fzhbioinfo]

Thank you for your response！

clinvar : https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/archive_2.0/2024/clinvar_20240107.vcf.gz
VEP & VEP cache : 110
input file : http://oss-fuyou-wgs.oss-cn-shenzhen.aliyuncs.com/public/1732845433/4087560226257100/input.vcf

with shift_3prime command :
singularity exec --bind /jdfstj4 vep.sif vep --cache --offline --dir_cache /jdfstj4/B2C_RD_R1/fangzhonghai/pipeline/test/vep/db/GRCh37/vep --tab --hgvs --refseq --exclude_predicted --no_escape --format vcf --fasta /jdfstj4/B2C_RD_R1/fangzhonghai/pipeline/test/vep/db/GRCh37/ref/ref.fa --assembly GRCh37 --custom file=/jdfstj4/B2C_RD_R1/fangzhonghai/pipeline/test/vep/db/GRCh37/vep/clinvar.vcf.gz,short_name=Clinvar,format=vcf,type=exact,fields=CLNSIG --shift_3prime 1 -i input.vcf -o with_shift_3prime_vep.tsv
with shift_3prime result file : http://oss-fuyou-wgs.oss-cn-shenzhen.aliyuncs.com/public/1732845564/94510807310021573/with_shift_3prime_vep.tsv

without shift_3prime command :
singularity exec --bind /jdfstj4 vep.sif vep --cache --offline --dir_cache /jdfstj4/B2C_RD_R1/fangzhonghai/pipeline/test/vep/db/GRCh37/vep --tab --hgvs --refseq --exclude_predicted --no_escape --format vcf --fasta /jdfstj4/B2C_RD_R1/fangzhonghai/pipeline/test/vep/db/GRCh37/ref/ref.fa --assembly GRCh37 --custom file=/jdfstj4/B2C_RD_R1/fangzhonghai/pipeline/test/vep/db/GRCh37/vep/clinvar.vcf.gz,short_name=Clinvar,format=vcf,type=exact,fields=CLNSIG -i input.vcf -o without_shift_3prime_vep.tsv
without shift_3prime result file : http://oss-fuyou-wgs.oss-cn-shenzhen.aliyuncs.com/public/1732845655/15615880100427010/without_shift_3prime_vep.tsv