Hi GATK team,
I was testing somatic CNV workflow in GATK 4.1. I found that CreateReadCountPanelOfNormals doesn't output valid HDF5 files. As an example, I have generated HDF5 files from three normal samples using CollectCounts, which can be found here:
https://www.dropbox.com/sh/lblf0u339t8asqo/AAA21rJSmtgRLfJw-fnEONwDa?dl=0
Then I tried to create PON from these file:
gatk --java-options -Xmx8g CreateReadCountPanelOfNormals --input 1302003-B-ready.counts.hdf5 --input 1436156-B-ready.counts.hdf5 --input 1436468-B-ready.counts.hdf5 --output example.hdf5
This command line runs without errors but resulting HDF5 could not be used by other functions such as DenoiseReadCounts. I noted that the three individual hdf5 files could be validated by hdfview (https://support.hdfgroup.org/products/java/hdfview/) but the one generated by CreateReadCountPanelOfNormals could not.
Can you help? Thanks,
Jiantao