The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
Input bam file for the CNN pipeline
I was looking to test the CNN pipeline and I saw that in the HC step was added the "-bamout" option (HC). To run the 2D model in the CNNScoreVariants tool I have to use as input bam file the original bam (post BQSR bam) or the bamout bam from the HC step?