Somatic Structure Variation on exome-seq data

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wiki97

• October 22, 2020 09:26
• Edited

category of my question: a)How do I (......)?

Hi, I am new to GATK exome-seq and would be grateful for any suggestions :)

I am planning to use GATK4 to perform Structure Variation analysis on whole-exome seq data (somatic).

My question is - is there any GATK pipeline available to perform such an analysis? 

I found this workflow: https://github.com/broadinstitute/gatk-sv

but this pipeline is designed for whole-genome seq, I found a note that it will not work for exome sequencing data..

I would be most grateful for any help :)

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  Genevieve Brandt (she/her)

  • October 30, 2020 16:06

  Hi wiki97,

  The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

  Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

  We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

  For context, check out our support policy.

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