The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
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