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CNV in GATK-126.96.36.199
I'm trying to perform copy number variation analysis on my BAM files. I started with this tutorial: https://gatkforums.broadinstitute.org/gatk/discussion/9143/how-to-call-somatic-copy-number-variants-using-gatk4-cnv/p1 but I found that some scripts (like CalculateTargetCoverage) are no longer used. I was wondering if there is an updated pipeline to perform the analysis.