varscan.v2.3.9 CNV call "Error: Invalid format or not enough samples in mpileup"
samtools mpileup -Avuf /oasis/projects/nsf/csd414/pdehoff/Reference/GRCh38_latest_genomic.fna hg38_synth.rd.bam Onco_comb_rd.bam | java -Xmx4G -jar /oasis/projects/nsf/csd414/pdehoff/programs/VarScan.v2.3.9.jar copynumber --mpileup Onco_hg38
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