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Old 04-06-2015, 11:05 AM   #18
etal
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Location: California

Join Date: Oct 2013
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What files were generated by the second run, if any? Can you show me the status messages or any errors that were printed?

When you run CNVkit with a reference, you don't need the "--targets", "--fasta", "--split" and "--access" arguments as that information has already been captured in the reference file. The default output directory is the current directory ("."). Try this instead:

cnvkit.py batch T1.bam T2.bam T3.bam T4.bam T5.bam T6.bam T7.bam T8.bam T9.bam T10.bam -r N.cnn --scatter --diagram
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