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Using ReducedReads as part of GATK pipeline

mpw6mpw6 Member
edited October 2012 in Ask the GATK team

We are attempting to see if using ReducedReads will help with the overwhelming file sizes for the SNP calling we are doing on whole genome BAM files. We have been using a protocol similar to the one described in best practices document: Best: multi-sample realignment with known sites and recalibration. My question is what is the best point in the pipeline to use ReducedReads?

Post edited by Geraldine_VdAuwera on

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