Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

DRAGMAP and Mutect?

Answered
0

3 comments

  • Official comment
    Avatar
    Genevieve Brandt (she/her)

    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

    Comment actions Permalink
  • Avatar
    Genevieve Brandt (she/her)

    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

    0
    Comment actions Permalink
  • Avatar
    rohit satyam

    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?

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk