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Old 03-12-2016, 06:10 PM   #38
etal
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Location: California

Join Date: Oct 2013
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You can skip bedcov with the -c/--count-reads option; it uses a different method to calculate read depths but should give similar results.

Also, if you've successfully built the target and antitarget BED files, you can use those as inputs to the "batch" command and drop some of the command line options:

cnvkit.py batch ~/MM02-N_MM02-020200/colossus_analysis/BAM/MM02-020200_MarkDup.bam --normal ~/MM02-N_MM02-020200/colossus_analysis/BAM/MM02-N_MarkDup.bam --targets results/Agilent_b37_exome_covered.target.bed --antitargets results/Agilent_b37_exome_covered.antitarget.bed --fasta ~/Ref/human_g1k_v37_decoy.fasta --output-reference my_reference.cnn --output-dir results/ --diagram --scatter --count-reads
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