Manually view the insert size and flag distribution results in the output. bam2cfgīam2cfg - create a configuration file for BreakDancer SYNOPSIS input_bams > config_file This step normally takes 12 hours or so for three bam files, 8 hours or so for two bam files for cpp version, around three days for perl version. The -d option dumps CTX supporting read pairs into fastq files (in this case BRC6.ctx) by library. usr/lib/breakdancer-max/ -g -h tumor.bam normal.bam > BRC6.cfgīreakdancer_max -t -q 10 -d BRC6.ctx BRC6.cfg > BRC6.ctx
#Bam file format column install#
The precompiled Debian package will install this in /usr/lib/breakdancer-max along with a few required Perl modules. STEP 1Ĭreate a configuration file using : Please see below for detailed information about the and breakdancer-max commands.
usr/lib/breakdancer-max1.2/ bam_files breakdancer_options See the below for parameter descriptions. To run BreakDancer, first use to prepare the required per-invocation config file.
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