filter_vep on HGNC_ID

[fellen31]

Describe the issue

Hi, I can't figure out how to use --filter "HGNC_ID in /test/hgnc.txt" when HGNC_ID is annotated as HGNC:12345 and not just 12345. I get no matching variants.

Thanks!

Additional information

Please fill in the following sections to help us find the source of your issue as quickly as possible.

System

• VEP version: 110
• VEP Cache version: 110 (GRCh38)
• Perl version: [e.g. 5.26]
• OS: [e.g. MacOS, Ubuntu, CentOS]
• tabix installed ?

Full VEP command line

 singularity exec --bind $(pwd):/test https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0 filter_vep --input_file /test/multisample_2.vcf.gz --filter "HGNC_ID in /test/hgnc.txt" --only_matched

Full error message

Including the warnings, if available

Data files (if applicable)

They include:

• The input file
• The output file
• The custom file(s)
  You can provide a sample of them

[likhitha-surapaneni]

Hi @fellen31,
Sorry to hear that you are facing issues with filtering. Can you please provide an input file you are using?

Thank you

[fellen31]

Sure, here's the file: multisample.vcf.gz

[likhitha-surapaneni]

Hi @fellen31, thank you for providing the input file. I am able to replicate the issue on my end.

We will try to provide a fix for this and keep you updated.

Kind regards,
Likhitha

[likhitha-surapaneni]

Hi @fellen31,

The fix will be made available in the coming release (release/113). I am closing this ticket for now. Please feel free to open a new issue if you are facing any other problems.

Thanks and regards,
Likhitha

[fellen31]

Thanks a lot @likhitha-surapaneni!