Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-08-07T14:29:53.917Z
Comments.Text: 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.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-08-07T21:38:13.470Z
Comments.Text: I use a template at biostars: https://www.biostars.org/p/9571077/#9571078
Comments.UserDisplayName: Ram RS
Tags: <variants><rna-splicing>
Title: spliceAI not giving output value while running using vep (Variant Ensemble Predictor)
ThreadText: # 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 @username_2. 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  
  
  ---
  
  ## 0 answers
  
  