SpliceVault Plugin giving empty results

[Ananya-Saji]

Hi,
We are currently using the VEP v115 Docker container to annotate VCF files. However, we are facing the following issues related to SpliceVault:

Here is the command I used to run VEP:
sudo docker run -i ensemblorg/ensembl-vep:release_115.2 vep -i input.vcf -o output.vcf --plugin SpliceVault,file=/path/to/SpliceVault_data_GRCh38.tsv.gz

Additionally, I tested the command below:
sudo docker run -i ensemblorg/ensembl-vep:release_115.2 vep --id "NM_001257386.2:c.1647+1G>A" -o output.vcf --plugin SpliceVault,file=/path/to/SpliceVault_data_GRCh38.tsv.gz

The results are given below -

Location	GIVEN_REF	Allele	Consequence	HGVSc	SpliceVault_SpliceAI_delta	SpliceVault_out_of_frame_events	SpliceVault_site_max_depth	SpliceVault_site_pos	SpliceVault_site_sample_count	SpliceVault_site_type	SpliceVault_top_events
chr4:88097452	C	T	splice_donor_variant	NM_001257386.2:c.1647+1G>A	-	-	-	-	-	-	-
chr4:88097452	C	T	splice_donor_variant	NM_001348985.1:c.1647+1G>A	-	-	-	-	-	-	-
chr4:88097452	C	T	splice_donor_variant	NM_001348986.1:c.1647+1G>A	-	-	-	-	-	-	-
chr4:88097452	C	T	splice_donor_variant	NM_001348987.1:c.1641+1G>A	-	-	-	-	-	-	-
chr4:88097452	C	T	splice_donor_variant	NM_001348988.1:c.1647+1G>A	-	-	-	-	-	-	-
chr4:88097452	C	T	splice_donor_variant	NM_001348989.2:c.1647+1G>A	-	-	-	-	-	-	-
chr4:88097452	C	T	splice_donor_variant	NM_004827.3:c.1647+1G>A	-	-	-	-	-	-	-
chr4:88097452	C	T	splice_donor_variant	XM_011532420.4:c.1647+1G>A	-	-	-	-	-	-	-
chr4:88097452	C	T	splice_donor_variant	XM_017008852.3:c.1641+1G>A	-	-	-	-	-	-	-

I am attaching SpliceVault online version's results below

Looking forward to your assistance. Thank you.

Best regards,
Ananya

[likhitha-surapaneni]

Hi @Ananya-Saji ,

Sorry to hear that you are facing issues.

The plugin matches based on the feature and it seems like the plugin contains Ensembl identifiers which may fail to match with Refseq identifiers if you are using --refseq in the command-line options.

Can you retry the command without refseq option as this enables Ensembl cache? You can also use --merged to use the merged Ensembl and RefSeq cache.

Let us know if this helps

[Ananya-Saji]

Hi @likhitha-surapaneni,

Thanks for your response. I tried using the RefSeq cache, and I will make the suggested changes and test it on my side.

Thank you for your help.