I'm trying to find CNV of our whole genome samples (split into 4 bam files). The first time I ran BAM2CFG and Breakdancer with NO option at all, and the output gave me interesting somatic CNVs also a huge collection of long CNVs and repeated CNVs which doesn't look too good. So I decided to trim out a bit and keep only good mapping quality CNVs. So far I was selecting with sed whatever has a mapping quality of 60 into each bam files. But then the CNV output was shorten to only 10% of what I had previously .. So doing again a selection with SED of reads mapped with a lower quality is gonna be a pain.
Can I use Breakdancer -m option to focus only on reads with a minimum mapping quality ? If I write the following :
breakdancer_max -m 40 file1.cfg > cnv.txt
Is it gonna for CNV among reads having a mapping quality of 40 and higher ? Is this method better than selecting out with sed everytime?