DRAGMAP and Mutect?

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registered_user

• January 26, 2022 13:21
• Edited

I was wondering if the open source DRAGMAP is currently compatible with Mutect? Is it possible to skip the BQSR step if using DRAGMAP instead of bwa-mem in PON creation and somatic variant calling with Mutect?

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• Official comment

  

  Genevieve Brandt (she/her)

  • February 01, 2022 17:33
  • Edited

  Hi registered_user,

  Thanks for writing in with this question! I asked our developer team who worked on DRAGEN-GATK. This is not something we have tested or verified but we think you could take advantage of the DRAGMAP aligner instead of running BWA. There would be a few differences in the tags and the mapping qualities would be different. Even with these differences, the DRAGMAP output should still be compatible with Mutect2.

  Unfortunately you would still need to use BQSR. The reason BQSR isn't needed anymore is because of changes in HaplotypeCaller that are not implemented in Mutect2. 

  Please let us know if you try this out and let me know if you have further questions.

  Best,

  Genevieve

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  Genevieve Brandt (she/her)

  • January 26, 2022 16:26

  Hi registered_user,

  I am going to move your post into our Community Discussions -> General Discussion topic, as the Somatic topic is for reporting bugs and issues with GATK.

  You can read more about our forum guidelines and the topics here: Forum Guidelines.

  Best,

  Genevieve

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  rohit satyam

  • October 09, 2022 08:27

  Genevieve Brandt (she/her) The Dragmap aligner isn't working properly anymore and when issues are posted on GitHub they aren't being attended to lately. It's been 2 months now. Since DragMap is DRAGEN-GATK's part is there any other way to get a functional dragmap aligner or a version of it that you guys use and maintain as part of your pipeline?

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