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broadinstitute / tgg_methods

Repo for miscellaneous methods developed by the methods group that don't fit anywhere else
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Generate sex and relatedness checks for old CMG projects #92

Closed jialanm closed 5 months ago

jialanm commented 5 months ago

Slack: https://the-tgg.slack.com/archives/D05LW43FMB8/p1710772620413789

Issue: A list of old CMG projects that will get released in AnVIL. PMs want to run sex and relatedness checks on the WGS samples in these projects.

Setbacks:

  1. There are 26 projects in the list and many of them have sample IDs that do not map to the sample IDs in the VCF callsets. It will require intense manual labor to re-map these sample IDs.
  2. The new pipeline performs automatic sex and relatedness checks and samples that pass the checks get loaded in seqr. In order to prevent the loading part, over 50 tasks need to be manually failed.
  3. PMs, ACBs, and SDEs were not on the same page with regard to the functions and workflow of the new seqr loading pipeline.

Solutions:

  1. Stacey, Ben B., and I had a sync meeting so that we all understood the changes and new workflow of the pipeline.
  2. We decided to run sex and relatedness checks on 2 projects only. The rest of the projects either did not need to be run or the s&r check results were already available. These 2 projects are: CMG_Lerner-Ellis_WGS and CMG_Wendy Chung_Genomes

Next Steps:

  1. Run s&r checks on the 2 projects with the new pipeline.

Notes:

  1. Assigned 8 effort points because there were many new issues due to the changes in the pipeline.