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Comments (7)

olaaustine avatar olaaustine commented on July 28, 2024

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.

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MGCarta avatar MGCarta commented on July 28, 2024

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

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olaaustine avatar olaaustine commented on July 28, 2024

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.

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olaaustine avatar olaaustine commented on July 28, 2024

Hi @MGCarta,
Hope you are well?
Just wanted up to follow up with this issue.
Thank you
Ola.

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MGCarta avatar MGCarta commented on July 28, 2024

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

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olaaustine avatar olaaustine commented on July 28, 2024

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.

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