Workflow for WES/WGS

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Sheryl

• September 15, 2023 01:27

I have used ExomeGermlineSingleSample_v3.1.9 wdl to create gVCFS.

Please can you confirm that I now need to consolidate the vcfs using GenomicsDBImport,

joint genotype using GenotypeGVCFs and filter with VariantRecalibrator and ApplyVQSR?

Are there current wdls available for these? The latest joint genotyping wdl that I could find was dated July 2022

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  Gökalp Çelik

  • October 03, 2023 11:42

  Hi Sheryl

  Yes you are right about the steps needed for followup. About the currentness of the workflows our suggestion would be to check the github page for warp pipelines.

  https://github.com/broadinstitute/warp 

  There you will also see readme files for changes for different workflows. 

  https://github.com/broadinstitute/warp/blob/develop/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md 

  I hope this helps. 

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