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Add vep sample #2384

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6418176
Merge pull request #1 from bihealth/main
ahujameg Apr 3, 2023
06ac783
Merge branch 'bihealth:main' into main
ahujameg Oct 12, 2023
3d04399
Merge branch 'bihealth:main' into main
ahujameg Nov 10, 2023
0d20feb
Merge branch 'varfish-org:main' into main
ahujameg Feb 7, 2024
9dc5248
docs: add sample VEP-annotated VCF for testing
boscoliveira Aug 8, 2025
fb347fc
Merge branch 'varfish-org:main' into add-vep-sample
boscoliveira Aug 8, 2025
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7 changes: 7 additions & 0 deletions VEP/HG008-T_vs_HG008-N-D.tnscope_VEP.ann.vcf
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Original file line number Diff line number Diff line change
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##fileformat=VCFv4.2
##reference=GRCh38
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|SYMBOL|Gene|Feature|Feature_type|HGVSc|HGVSp|gnomAD_AF|CLIN_SIG">
#CHROM POS ID REF ALT QUAL FILTER INFO
17 43094464 rs80357914 C T . PASS CSQ=T|missense_variant|BRCA1|ENSG00000012048|NM_007294.4|Transcript|NM_007294.4:c.5266C>T|p.Arg1756His|0.00001|likely_pathogenic
2 189873659 rs123456789 A T . PASS CSQ=T|splice_region_variant|COL5A2|ENSG00000163083|NM_000393.5|Transcript|NM_000393.5:c.1158+5A>T|-|0.0001|uncertain_significance
17 3634395 rs987654321 GAT G . PASS CSQ=T|inframe_deletion|CTNS|ENSG00000103175|NM_004937.3|Transcript|NM_004937.3:c.614_616del|p.Asp205del|0.0008|pathogenic
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💡 Verification agent

❓ Verification inconclusive

CSQ Allele does not match ALT (data correctness).

For this record, REF=GAT and ALT=G, but CSQ starts with T as the Allele. The CSQ Allele field must match ALT.

Apply this diff to fix the allele:

-17	3634395	rs987654321	GAT	G	.	PASS	CSQ=T|inframe_deletion|CTNS|ENSG00000103175|NM_004937.3|Transcript|NM_004937.3:c.614_616del|p.Asp205del|0.0008|pathogenic
+17	3634395	rs987654321	GAT	G	.	PASS	CSQ=G|inframe_deletion|CTNS|ENSG00000103175|NM_004937.3|Transcript|NM_004937.3:c.614_616del|p.Asp205del|0.0008|pathogenic

Optional quick check to validate CSQ Allele equals ALT for all records (assumes single ALT and single CSQ entry per record):

🏁 Script executed:

#!/bin/bash
awk -F'\t' 'BEGIN{err=0} !/^#/ {
  alt=$5;
  info=$8;
  csq="";
  n=split(info,a,";");
  for(i=1;i<=n;i++){ if(a[i] ~ /^CSQ=/){ csq=substr(a[i],5); break } }
  if(csq=="") next;
  split(csq,f,"|");
  allele=f[1];
  if(allele!=alt){ 
    printf("Allele mismatch at %s:%s ALT=%s CSQ_Allele=%s\n",$1,$2,alt,allele) > "/dev/stderr"; 
    err=1 
  }
} END{ exit err }' VEP/HG008-T_vs_HG008-N-D.tnscope_VEP.ann.vcf

Length of output: 459

Fix CSQ Allele mismatch

Verification confirmed a CSQ Allele of “T” does not match the ALT (“G”) at chr17:3634395. Update the CSQ field to use the ALT allele:

• File: VEP/HG008-T_vs_HG008-N-D.tnscope_VEP.ann.vcf
• Location: record at 17:3634395

Diff:

-17	3634395	rs987654321	GAT	G	.	PASS	CSQ=T|inframe_deletion|CTNS|ENSG00000103175|NM_004937.3|Transcript|NM_004937.3:c.614_616del|p.Asp205del|0.0008|pathogenic
+17	3634395	rs987654321	GAT	G	.	PASS	CSQ=G|inframe_deletion|CTNS|ENSG00000103175|NM_004937.3|Transcript|NM_004937.3:c.614_616del|p.Asp205del|0.0008|pathogenic
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Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
17 3634395 rs987654321 GAT G . PASS CSQ=T|inframe_deletion|CTNS|ENSG00000103175|NM_004937.3|Transcript|NM_004937.3:c.614_616del|p.Asp205del|0.0008|pathogenic
17 3634395 rs987654321 GAT G . PASS CSQ=G|inframe_deletion|CTNS|ENSG00000103175|NM_004937.3|Transcript|NM_004937.3:c.614_616del|p.Asp205del|0.0008|pathogenic
🤖 Prompt for AI Agents 
In VEP/HG008-T_vs_HG008-N-D.tnscope_VEP.ann.vcf at line 7, the CSQ field allele
"T" does not match the ALT allele "G" for the variant at chr17:3634395. Update
the CSQ field to replace the allele "T" with the correct ALT allele "G" to
ensure consistency between the CSQ annotation and the ALT allele.

5 changes: 5 additions & 0 deletions VEP/sample_vep.txt
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## VEP output generated at 2025-01-28 19:30:00
## Using cache in /cache
## Command: vep --input_file variant_input.txt --output_file variant_output.txt --format vcf --tab --force_overwrite --species homo_sapiens --assembly GRCh38 --offline --cache --symbol --hgvs --hgvsc --hgvsp --af_gnomad --clin_sig
#Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation Extra HGVSc HGVSp gnomAD_AF CLIN_SIG
COL5A2_variant 2:189873659 T COL5A2 NM_000393.5 Transcript splice_region_variant 1158+5 - - - - rs123456789 SYMBOL=COL5A2;SYMBOL_SOURCE=HGNC;HGNC_ID=HGNC:2210 NM_000393.5:c.1158+5A>T - 0.0001 uncertain_significance
5 changes: 5 additions & 0 deletions VEP/sample_vep_small.txt
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## VEP output generated at 2025-01-28 19:30:00
## Using cache in /cache
## Command: vep --input_file variant_input.txt --output_file variant_output.txt --format vcf --tab --force_overwrite --species homo_sapiens --assembly GRCh38 --offline --cache --symbol --hgvs --hgvsc --hgvsp --af_gnomad --clin_sig
#Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation Extra HGVSc HGVSp gnomAD_AF CLIN_SIG
COL5A2_variant 2:189873659 T COL5A2 NM_000393.5 Transcript splice_region_variant 1158+5 - - - - rs123456789 SYMBOL=COL5A2;SYMBOL_SOURCE=HGNC;HGNC_ID=HGNC:2210 NM_000393.5:c.1158+5A>T - 0.0001 uncertain_significance
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