GATK4: Trouble running "GATK 4 CNV Proportional Coverage for Capture"

Hi,

I am trying to run "GATK 4 CNV Proportional Coverage for Capture" on
samples with no matched normals sequenced using TSCA (TrueSeq Custom
Capture).

I understand that the first step is to run "GATK 4 CNV Proportional
Coverage for Capture" and configure the task replacing
gatk4cnv_padded_target_bed_capture with the bed file with the intervals
covered.

I am getting the attached error and stdout. It seems that it doesn't like
the fact that some intervals are overlapping. What is the workaround to
this?

I am running GATK4 workflow because I would like to run absolute to
estimate the purity of the samples. If there is a simpler way to get the
purity of such samples, please let me know.

Thanks,

Sahar