Generating COSMIC.db Data Source for Funcotator

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Kaina Millan

• January 16, 2025 20:00

Hello, 

I am currently using Funcotator's  (GATK4.6.1) v1.8 data source to annotate somatic variants after using Mutect2. I noticed that the COSMIC data source is v98, while the COSMIC site currently uses v101. I attempted to download a COSMIC VCF file and generate my own configuration file to annotate with Funcotator, but that did not seem to work. I am wondering if COSMIC annotations can only be added using files with the extension ".db" since this is how the COSMIC data source from Funcotator seems to have been generated. 

If that is the case, would you be able to provide any advice as to how to annotate my variants with the most updated version of COSMIC?

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  Gökalp Çelik

  • January 27, 2025 18:01

  Hi Kaina Millan

  We have scripts to produce our data sources for funcotator and specifically the script named 

  https://github.com/broadinstitute/gatk/blob/master/scripts/funcotator/data_sources/cosmic/getCosmicDataSources.sh 

  can get the Cosmic data for you and creates necessary files for funcotator. Our code is valid upto version 98 and we don't expect anything to be too different with version 101. However we have not tested it and we cannot provide any support directly on data sources that are not produced by us. 

  Keep in mind that this code requires you to have your own COSMIC account for downloads therefore it is your responsibility to get a valid token to access the downloadable data. 

  I hope this helps.

  Regards. 

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  Kaina Millan

  • January 27, 2025 19:15

  I will go ahead and give this a try- thank you so much for your help!

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  yinxiu Zhan

  • January 02, 2026 19:24

  Hi there,

  Cosmic, after beeing acquired by QIAGEN, changed both the sources path and slightly the sources format. Are you guys planning to adapt the getCosmicDataSources.sh  accordingly?

  Thanks
  Best

  Zhan

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