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GermlineCNVCaller --interval-merging-rule error.
I was testing the brand new GermlineCNVCaller in 18.104.22.168 however I met a very strange error.
All my read collections was made with the following command
gatk CollectReadCounts -R $HG19FULL --interval-merging-rule OVERLAPPING_ONLY -L $TSOREG -I samplename_final.bam -O samplename_counts.hdf5
And there was no problem with DetermineGermlineContigPloidy step. All files were generated using GATK 22.214.171.124 docker image fresh from docker repo.
DetermineGermlineContigPloidy command was according to the doc files within the gatk folder. I have 32 samples and I was working in COHORT mode.
Here is the error message
Where is the problem here?