The frontline support team will be offline as we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and available to answer questions on the forum on March 25th 2019.
Hi GATK team,
I am trying to do downsample analysis using gatk PrintReads. The GATK version is 184.108.40.206.
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.