If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 18.104.22.168
b) Exact command used: java -jar gatk-package-22.214.171.124-local.jar DepthOfCoverage -R ucsc.hg19.fasta -I 1.bam -O 1_pregatk_base -L 2.bed -ct 125 >& depthofcoverage.log
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):
I'd like to get the percent of reads under the threshold using -ct or -summary-coverage-threashold as I did in previous version.
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