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how to do downsampling
Could anyone tell me how to do downsampling analysis by using GATK tools? The GATK version I use is 188.8.131.52.
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 kindly help?
Thank you very much.