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Haplotype Caller -dcov flag

Is there any way to override/re-implement the -dcov flag (which has been removed from the haplotype caller). I have a region that is almost 700 base pairs deep and continually causes a memory overload error. How can I restrict the coverage depth effectively?



Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,557Administrator, Dev admin

    Hi Paul,

    What version are you using? The -dcov option is available in the current version, which is 2.6-4.

    Geraldine Van der Auwera, PhD

  • pauljpembertonpauljpemberton Posts: 6Member

    I am using GATK v2.5-2, maybe it is just the online documentation that is missing the -dcov discription, but I was unable to discern whether or not -dcov refers to the number of reads starting at a single location (i.e. -dcov = 2 would only allow 2 reads to begin at the same place), or if it refers to the number of reads at any location (i.e. -dcov =2 would only allow 2 reads to appear at a specific location in the genome).


  • pauljpembertonpauljpemberton Posts: 6Member

    Perfect, thanks for the quick responses!

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