Conversation
WalkthroughThree new files have been added under the VEP directory: a VCF file with Ensembl VEP annotations for multiple variants, and two VEP output files containing variant annotation results for single variants. All files include detailed variant consequence annotations, allele frequencies, and clinical significance information. Changes
Estimated code review effort🎯 1 (Trivial) | ⏱️ ~3 minutes Poem
Note 🔌 MCP (Model Context Protocol) integration is now available in Early Access!Pro users can now connect to remote MCP servers under the Integrations page to get reviews and chat conversations that understand additional development context. ✨ Finishing Touches🧪 Generate unit tests
Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out. 🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
SupportNeed help? Create a ticket on our support page for assistance with any issues or questions. CodeRabbit Commands (Invoked using PR comments)
Other keywords and placeholders
CodeRabbit Configuration File (
|
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
There was a problem hiding this comment.
Actionable comments posted: 2
🔭 Outside diff range comments (2)
VEP/sample_vep.txt (1)
6-6: Remove stray trailing character line.There's a lone "6" at the end of the file. This will confuse simple TSV parsers and is likely accidental.
Apply this diff to remove it:
-6 +VEP/sample_vep_small.txt (1)
6-6: Remove stray trailing character line.Identical issue as in sample_vep.txt: a lone "6" at EOF will break parsing.
Apply this diff to remove it:
-6 +
🧹 Nitpick comments (1)
VEP/HG008-T_vs_HG008-N-D.tnscope_VEP.ann.vcf (1)
1-4: Optional: add contig headers for stricter validators.Consider adding
##contiglines for referenced chromosomes (e.g., 2, 17) to satisfy tools that expect them for GRCh38.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (3)
VEP/HG008-T_vs_HG008-N-D.tnscope_VEP.ann.vcf(1 hunks)VEP/sample_vep.txt(1 hunks)VEP/sample_vep_small.txt(1 hunks)
🧰 Additional context used
🧠 Learnings (2)
📓 Common learnings
Learnt from: holtgrewe
PR: varfish-org/varfish-server#1957
File: backend/external-copy-0.vcf:0-0
Timestamp: 2024-10-10T10:46:51.742Z
Learning: In the Varfish server repository, some VCF files like `backend/external-copy-0.vcf` contain example data. It's acceptable for these files to include absolute paths in their VCF headers.
📚 Learning: 2024-10-10T10:46:51.742Z
Learnt from: holtgrewe
PR: varfish-org/varfish-server#1957
File: backend/external-copy-0.vcf:0-0
Timestamp: 2024-10-10T10:46:51.742Z
Learning: In the Varfish server repository, some VCF files like `backend/external-copy-0.vcf` contain example data. It's acceptable for these files to include absolute paths in their VCF headers.
Applied to files:
VEP/HG008-T_vs_HG008-N-D.tnscope_VEP.ann.vcf
🔇 Additional comments (1)
VEP/sample_vep.txt (1)
2-3: Absolute paths in sample metadata are acceptable here.The cache path and command metadata look fine for sample data in this repo (see prior acceptance of absolute paths in sample VCF headers).
| #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 |
There was a problem hiding this comment.
💡 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|pathogenicOptional 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.vcfLength 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📝 Committable suggestion
‼️ IMPORTANT
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.
| 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.
| ## 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 |
There was a problem hiding this comment.
💡 Verification agent
🧩 Analysis chain
Avoid duplicating identical sample files.
This file is identical to VEP/sample_vep.txt. Consider keeping only one sample (or documenting how they differ) to prevent divergence over time.
Quick check for duplication:
🏁 Script executed:
#!/bin/bash
diff -u VEP/sample_vep.txt VEP/sample_vep_small.txt || trueLength of output: 53
🏁 Script executed:
#!/bin/bash
# Verify that both sample files exist and compare their sizes, hashes, and first few lines
# Check for existence
echo "Checking file existence:"
ls -l VEP/sample_vep.txt VEP/sample_vep_small.txt || exit 1
# Compare file sizes
echo -e "\nFile sizes:"
stat --format="%n %s bytes" VEP/sample_vep.txt VEP/sample_vep_small.txt
# Compute MD5 hashes
echo -e "\nMD5 checksums:"
md5sum VEP/sample_vep.txt VEP/sample_vep_small.txt
# Show first 5 lines of each
echo -e "\nFirst 5 lines of sample_vep.txt:"
head -n 5 VEP/sample_vep.txt
echo -e "\nFirst 5 lines of sample_vep_small.txt:"
head -n 5 VEP/sample_vep_small.txtLength of output: 2333
Consolidate duplicate sample files in VEP/
Our checks confirmed that VEP/sample_vep.txt and VEP/sample_vep_small.txt are byte-for-byte identical. To prevent them drifting apart over time, please keep only one of these samples (or explicitly document any intended differences).
• Remove or archive one of:
- VEP/sample_vep.txt
- VEP/sample_vep_small.txt
🤖 Prompt for AI Agents
In VEP/sample_vep_small.txt around lines 1 to 5, the file is byte-for-byte
identical to VEP/sample_vep.txt, causing unnecessary duplication. To fix this,
remove or archive one of these files to prevent them from drifting apart over
time, keeping only a single canonical sample file or clearly documenting any
intended differences if both are to be retained.
2 participants
Summary by CodeRabbit