The Frontline Support team will be slow to respond December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks. Happy Holidays!
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