<p>While generating the predictions using spliceAI from vep, I am not getting any values.</p>
<p>I used this command to generate the output,</p>
<pre><code>vep \
  -i input.vcf \
  -o output.vcf \
  --cache \
  --force_overwrite \
  --tab \
  --no_check_variants_order \
  --force \
  --plugin SpliceAI,snv=spliceai_scores.raw.snv.hg38.vcf.gz,indel=spliceai_scores.raw.indel.hg38.vcf.gz
</code></pre>
<p>Below, are the examples of entries in the output file.</p>
<pre><code>ENSEMBL VARIANT EFFECT PREDICTOR v109.3  
Output produced at 2023-08-07 09:05:43  
Connected to homo_sapiens_core_109_38 on ensembldb.ensembl.org  
Using cache in /.vep/homo_sapiens/109_GRCh38  
Using API version 109, DB version 109  
ensembl-io version 109.4946a86  
ensembl version 109.10baaec  
ensembl-funcgen version 109.cba2db8  
ensembl-variation version 109.18a12b6  
...  
Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation IMPACT DISTANCE STRAND FLAGS SpliceAI_pred  
100017682 chr1:100017682 A ENSG00000117620 ENST00000370153 Transcript missense_variant,splice_region_variant 981 880 294 A/T Gca/Aca - MODERATE - -     
100017682 chr1:100017682 A ENSG00000117620 ENST00000370155 Transcript splice_region_variant,3_prime_UTR_variant,NMD_transcript_variant 882 - - - - LOW - 1 - -
</code></pre>
<p>Is there any wrong in the input file? Could anyone help here?</p>

CC BY-SA 4.0
2023-08-07T14:29:53.917Z
Thanks (again) for editing this @RamRs. We need to make documentation (meta-post) for new member's code format .... in fact this is particularly well edited and like to use this as the example for a meta post.
M__
CC BY-SA 4.0
2023-08-07T21:38:13.470Z
I use a template at biostars: https://www.biostars.org/p/9571077/#9571078
Ram RS
<variants><rna-splicing>
spliceAI not giving output value while running using vep (Variant Ensemble Predictor)
# spliceAI not giving output value while running using vep (Variant Ensemble Predictor)

(Asked by: username_0 on 2023-08-07)

While generating the predictions using spliceAI from vep, I am not getting any values.
I used this command to generate the output,
vep \
  -i input.vcf \
  -o output.vcf \
  --cache \
  --force_overwrite \
  --tab \
  --no_check_variants_order \
  --force \
  --plugin SpliceAI,snv=spliceai_scores.raw.snv.hg38.vcf.gz,indel=spliceai_scores.raw.indel.hg38.vcf.gz

Below, are the examples of entries in the output file.
ENSEMBL VARIANT EFFECT PREDICTOR v109.3  
Output produced at 2023-08-07 09:05:43  
Connected to homo_sapiens_core_109_38 on ensembldb.ensembl.org  
Using cache in /.vep/homo_sapiens/109_GRCh38  
Using API version 109, DB version 109  
ensembl-io version 109.4946a86  
ensembl version 109.10baaec  
ensembl-funcgen version 109.cba2db8  
ensembl-variation version 109.18a12b6  
...  
Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation IMPACT DISTANCE STRAND FLAGS SpliceAI_pred  
100017682 chr1:100017682 A ENSG00000117620 ENST00000370153 Transcript missense_variant,splice_region_variant 981 880 294 A/T Gca/Aca - MODERATE - -     
100017682 chr1:100017682 A ENSG00000117620 ENST00000370155 Transcript splice_region_variant,3_prime_UTR_variant,NMD_transcript_variant 882 - - - - LOW - 1 - -

Is there any wrong in the input file? Could anyone help here?

**Tags:** variants, rna-splicing
> **Comments:**
> **username_1**: Thanks (again) for editing this @RamRs. We need to make documentation (meta-post) for new member's code format .... in fact this is particularly well edited and like to use this as the example for a meta post.  
> **username_2**: I use a template at biostars: https://www.biostars.org/p/9571077/#9571078  

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## 0 answers

