VariantToTable_ Errors in the Tab delimited output

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Aditya Saxena

• January 16, 2025 16:52

REQUIRED for all errors and issues:
a) GATK version used: 4.6.1.0
b) Exact command used: attached
c) Entire program log: attached 
I am running gatk via docker. I was able to convert a .vcf file from ClinVar to a tab-delimited table with VariantsToTable function.

However, the Clinical Significance field (CLNSIG) with word entries (e.g. Uncertain_significance or Likely_benign) in the input instead has a range of numeric enteries (attached output table pic) in the output. Can you please guide me to troubleshoot this. 

 

Thanks,

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  Gökalp Çelik

  • January 16, 2025 18:45

  Hi Aditya Saxena

  Can you share some of the variant context from the original file to see if CLNSIG field is populated with string or numeric arrays? I am unable to replicate this issue so it could be your input VCF that has some different formatting inside.

   

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  Aditya Saxena

  • January 16, 2025 18:53
  • Edited

  Thanks Gokalp!!

  Here is the original vcf file that I used as input:

  https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/archive_2.0/2024/clinvar_20241223.vcf.gz

  appreciate your help. 

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  Gökalp Çelik

  • January 18, 2025 17:49

  Hi again. 

  The source file you pointed at did not reproduce the issue you are facing. Are you sure that you are not using another VCF file edited/created using this original source? It is possible that those entries might have been converted to enumerated types of integer references instead of keeping them as strings. This is the result from the first 50000 lines from the file. 

  

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