calling large scale structural variants

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lid.zigh

• August 26, 2021 12:21

a)How do I call large scale structural variants using GATK version 4.2 and which command line I need to use? 

Thank you,

Lida 

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  Genevieve Brandt (she/her)

  • August 31, 2021 18:32

  Hi lid.zigh,

  Calling structural variants uses multiple GATK tools so we have pipelines for this method. Our most up to date pipeline is uses WDL and can be found here: https://github.com/broadinstitute/gatk-sv. Another option is the StructuralVariationDiscoveryPipelineSpark, which can be found here: https://gatk.broadinstitute.org/hc/en-us/articles/4405443715611-StructuralVariationDiscoveryPipelineSpark-BETA-

  They are both still in the development stage, though I believe the most attention from our team is focused on the gatk-sv WDL methods.

  Hope this helps, let me know if you have any other questions.

  Best,

  Genevieve

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