Somatic Calling with Mutect2

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John

• June 18, 2024 11:52

Hello, 

I am using Mutect2 to identify variants in my files. I did all the preprocessing steps: Aligned with BWA, Added RG, MarkDuplicates, Base Recalibration. After this, I am using Mutect2 and FilterMutectCalls. When searching for a complete pipeline for mutect2, all I can only see is a pipeline for HaplotypeCaller, wherre they used GenotypeGVCFs for joint variant callings. Is it something that applies for Mutect2 pipeline. What about the Variant Recalibration? Should it be used?

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  Gökalp Çelik

  • June 18, 2024 14:49
  • Edited

  Hi John

  Mutect2 workflow does not include any joint calling steps therefore you need to call variants with Mutect2 and use FilterMutectCalls to filter your variants. There is no variant recalibration or GVCF genotyping step included. 

  Our workflows are usually included in the WARP site and within github page for GATK

  https://github.com/broadinstitute/gatk/blob/master/scripts/mutect2_wdl/mutect2.wdl 

  https://broadinstitute.github.io/warp/docs/Pipelines/Genomic_Data_Commons_Whole_Genome_Somatic/README 

  Keep in mind that these are recommendations but not absolute solutions that fits all use cases. You may need to modify certain parameters for your own use case. 

  I hope this helps.

  Regards. 

   

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