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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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batch creates FASTA's bed in working dir not in output-dir #781

Open solo7773 opened 1 year ago

solo7773 commented 1 year ago

version 0.9.9

cnvkit.py batch --normal $normal --fasta $fasta --output-dir $outdir -m wgs

I use the above command to generate the reference.cnn. The command runs in a computing cluster via qsub. The command runs as expected, excepting a file named $fasta.bed is generated in the working dir. I checked and found it's the output of the access subcommand. Could you fix this bug, although it's not fatal?