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Hi GATK team,
I am trying to do downsample analysis using gatk PrintReads. The GATK version is 18.104.22.168.
Below is my command:
gatk PrintReads -R path/to/hg19.fa -I LIB.bam -O LIB_downsample10.bam --downsample_to_coverage 10
But it always threw out this error:
A USER ERROR has occurred: downsample_to_coverage is not a recognized option
When I changed the '--downsample_to_coverage' to '-dcov', the error became this:
A USER ERROR has occurred: d is not a recognized option
Could you please help?
Thank you very much.