Comments (7)
HI @MGCarta,
Hope this meets you well 😊
Thank you for your query.
Is it possible to share the full VEP command used?
Thank you
Ola.
from vep_plugins.
Yes, sorry! I am using vep 110.1 and the command is:
vep --offline \
--cache \
--fork 4 \
--assembly GRCh38 \
--refseq \
--force_overwrite \
--symbol \
--canonical \
--mane \
--numbers \
--no_intergenic \
--clin_sig_allele 1 \
--af \
--af_1kg \
--af_gnomade \
--af_gnomadg \
--pubmed \
--vcf \
--dir $4 \
--fasta ./vep/.vep/homo_sapiens/110_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz \
--input_file $1 \
--plugin dbNSFP,./vep/.vep/Plugins/dbNSFP/dbNSFP4.5a_grch38.gz,pep_match=0,SIFT_converted_rankscore,Polyphen2_HDIV_rankscore,Polyphen2_HVAR_rankscore,LRT_converted_rankscore,MutationTaster_converted_rankscore,MutationAssessor_rankscore,FATHMM_converted_rankscore,PROVEAN_converted_rankscore,MetaSVM_rankscore,M-CAP_rankscore,REVEL_rankscore,MutPred_rankscore,CADD_raw_rankscore,DANN_rankscore,fathmm-MKL_coding_rankscore,fathmm-XF_coding_rankscore,GM12878_fitCons_rankscore,GERP++_RS_rankscore,phyloP100way_vertebrate_rankscore,phyloP17way_primate_rankscore,phastCons100way_vertebrate_rankscore,phastCons17way_primate_rankscore \
--plugin SpliceAI,snv=./vep/.vep/Plugins/spliceAI/spliceai_scores.raw.snv.hg38.vcf.gz,indel=./vep/.vep/Plugins/spliceAI/spliceai_scores.raw.indel.hg38.vcf.gz,cutoff=0.5 \
--plugin SingleLetterAA \
--output_file $3
from vep_plugins.
Hi @MGCarta,
I have not been able to replicate this issue.
When i run it with the SingleLetterAA plugin, i get
7_140778037_TAGGTGCTGTCACAT/- 7:140778037-140778051 - 673 NM_004333.6 Transcript inframe_deletion 1683-1697 1457-1471 486-491 NVTAPT/T aATGTGACAGCACCTAca/aca - IMPACT=MODERATE;STRAND=-1;SYMBOL=BRAF;SYMBOL_SOURCE=EntrezGene;CANONICAL=YES;MANE_SELECT=ENST00000646891.2;GIVEN_REF=TAGGTGCTGTCACAT;USED_REF=TAGGTGCTGTCACAT;EXON=12/18;HGVSp=NP_004324.2:p.N486_P490del
and when I run without the plugin and just the command --hgvs
I get
7_140778037_TAGGTGCTGTCACAT/- 7:140778037-140778051 - 673 NM_004333.6 Transcript inframe_deletion 1683-1697 1457-1471 486-491 NVTAPT/T aATGTGACAGCACCTAca/aca - IMPACT=MODERATE;STRAND=-1;SYMBOL=BRAF;SYMBOL_SOURCE=EntrezGene;CANONICAL=YES;MANE_SELECT=ENST00000646891.2;GIVEN_REF=TAGGTGCTGTCACAT;USED_REF=TAGGTGCTGTCACAT;EXON=12/18;HGVSc=NM_004333.6:c.1457_1471del;HGVSp=NP_004324.2:p.Asn486_Pro490del
Please can you use the command --dir_plugins to see if this issue still persists and if it does can you let us know the versions of cache, you are using.
Thank you very much
Ola.
from vep_plugins.
Hi @MGCarta,
Hope you are well?
Just wanted up to follow up with this issue.
Thank you
Ola.
from vep_plugins.
Hi @olaaustine, sorry for my late reply!
I tried to set the parameter
--dir_plugins ./vep/.vep/Plugins
but I still get the same HGVSp:
7 | 140778036 | 7_140778037_TAGGTGCTGTCACAT/- | GTAGGTGCTGTCACAT | G | . | . | Canonical | 19 | inframe_deletion | BRAF | 12/18 | | NM_004333.6:c.1457_1471del | NP_004324.2:p.NVT486_APT491delinsT | NP_004324.2:p.NVT486_APT491delinsT | NVTAPT/T | rs1586126439 | YES | | | | | | | | | | | | | | | | | |
The version of the cache is 110_GRCh38
from vep_plugins.
Hi @MGCarta,
Thank you for your response.
Please is it possible to use the latest version of VEP plugins that is release/111.
This issue has been fixed for this version.
Do let us know if this resolves the issue.
Thank you very much
Ola.
from vep_plugins.
Related Issues (20)
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