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Old 04-06-2015, 10:44 AM   #17
lethalfang
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Location: San Francisco, CA

Join Date: Aug 2011
Posts: 95
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When I tried to run more tumor samples using the reference .cnn file from a past normal run, there is no .cnr output.

This gives me .cnr files:
cnvkit.py batch T1.bam T2.bam T3.bam T4.bam T5.bam T6.bam T7.bam T8.bam T9.bam T10.bam --normal Na.bam Nb.bam Nc.bam --targets captures.bed --fasta b37_decoy.fasta --split --access b37.decoy.accessibles.bed --scatter --diagram --output-reference N.cnn --output-dir .


This does not output .cnr pr antitargetcoverage.cnn file:
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 --targets captures.bed --fasta b37_decoy.fasta --split --access b37.decoy.accessibles.bed --scatter --diagram --output-dir .

What is missing? Thanks.
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