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Removing * Alleles


The program I am using for analysis considers * alleles inappropriate for analysis. From my understanding these are spanning deletions, but I am unsure how to properly remove them from my data.

Do you have any recommendations for how I can effectively remove these alleles from my dataset? I've tried every recommendation based on a search in this forum including -selectTypeToExclude MIXED --selectTypeToExclude SYMBOLIC but to no avail.



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Unfortunately we currently don't have a good way to remove those records through GATK, but we have a ticket to add functionality to that effect.

    I believe others have posted about using unix command line utilities to do this.

    Regardless of how you choose to proceed, I would strongly encourage you to write to the authors of the software you want to use next and ask them to make their program handle spanning deletions (if only by ignoring those records).
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