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Is --downsample_to_fraction available for GATK 4.0?


Is their any equivalent flag to --downsample_to_fraction for GATK 4 (for example when running BaseRecalibrator)?



  • SheilaSheila Broad InstituteMember, Broadie, Moderator


    You can check the tool docs to see which available arguments there are. In GATK4, the tool docs include all possible arguments for each tool. In the case of BaseRecalibrator, there is no downsampling argument (I suspect because tool needs to see all possible bases at the site).


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    To downsample a bam, we now recommend running the Picard tool DownsampleBam (which you can use from within GATK4) to generate a downsampled file up front.

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