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Recommendation / best practices GVCF GQ bands
Dear GATK team,
Do you have any recommendation or best practice guidelines on the GVCFGQBands setting? This used to be (gatk < 3.2) [0,5,20,60] but has been changed one block per GQ value in gatk > 3.3. We would like to decrease the file size of the g.vcf files without loosing to much resolution / sensitivity. In the gvcf docs the 'old' defaults are still mentioned: https://www.broadinstitute.org/gatk/guide/article?id=4017