The frontline support team will be unavailable to answer questions on April 15th and 17th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!
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