If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: gatk-4.1.7.0
b) Exact command used:

java -Xmx25g -jar /garnet/Tools/WGS_Analysis/Program/GATK/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar DepthOfCoverage -R /garnet/Tools/WGS_Analysis/DB_Analy/iSAAC/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -I Free_550_2_2.recal.bam -O ./new/Free_550_2_2.recal.depcov -ct 1 -ct 2 -ct 5 -ct 10 -ct 15 -ct 20 -ct 30 -ct 40 -ct 50 -L /garnet/Tools/WGS_Analysis/DB_Analy/iSAAC/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/Homosapiens_hg19.bed --omit-depth-output-at-each-base true --omit-interval-statistics true

c) Entire error log:

***********************************************************************

A USER ERROR has occurred: c is not a recognized option

***********************************************************************

If not an error, choose a category for your question(REQUIRED):
c) Why do I see (these error message)?
 

In GATK4 beta manual page, We found these parameter usage in depth of coverage.....

When I tried to use above command, I got an error message. 

As you can see my command line, I could not type the 'c' option.

But, if I tired to command without "-ct option", it worked well.

Could you give me some advice about this problem?

Thank you,

============================================================

I solved this problem by using --summary-coverage-threshold option instead '-ct' like this

"--summary-coverage-threshold 1 --summary-coverage-threshold 2 --summary-coverage-threshold 5 --summary-coverage-threshold 10 ..."

I remain this post for other people who suffer the same issue.

Thank you,