Hi !
CNVkit helps me a lot, thank you at first.
When I tried to build my normal reference, I found some bins that failed filters.
My command:
cnvkit.py batch -n [bams of normal samples] -f /ref/hg19/hg19.fasta -p 16 -t [my target bed] -g [my target bed]
Then I got:
Targets: 21 (3.8043%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0)ALK chr2:30143077-30143308 log2=0.364 spread=0.206 rmask=nan" chr2:30143309-30143540 log2=0.391 spread=0.160 rmask=nan....CDKN2A chr9:21970887-21971222 log2=0.462 spread=0.178 rmask=nan" chr9:21974663-21974846 log2=-0.683 spread=0.246 rmask=nanBRCA2 chr13:32906395-32906680 log2=-0.150 spread=0.123 rmask=nan" chr13:32912215-32912475 log2=-0.598 spread=0.285 rmask=nan" chr13:32918681-32918805 log2=-0.325 spread=0.195 rmask=nanERBB2 chr17:37856478-37856579 log2=0.155 spread=0.108 rmask=nan
The thing is, none of those looks like a bad bin...
Their log2 & spread looks OK...
Why ?
How to fix it ?
Hi ! CNVkit helps me a lot, thank you at first. When I tried to build my normal reference, I found some bins that failed filters. My command:
cnvkit.py batch -n [bams of normal samples] -f /ref/hg19/hg19.fasta -p 16 -t [my target bed] -g [my target bed]Then I got:Targets: 21 (3.8043%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0)ALK chr2:30143077-30143308 log2=0.364 spread=0.206 rmask=nan" chr2:30143309-30143540 log2=0.391 spread=0.160 rmask=nan....CDKN2A chr9:21970887-21971222 log2=0.462 spread=0.178 rmask=nan" chr9:21974663-21974846 log2=-0.683 spread=0.246 rmask=nanBRCA2 chr13:32906395-32906680 log2=-0.150 spread=0.123 rmask=nan" chr13:32912215-32912475 log2=-0.598 spread=0.285 rmask=nan" chr13:32918681-32918805 log2=-0.325 spread=0.195 rmask=nanERBB2 chr17:37856478-37856579 log2=0.155 spread=0.108 rmask=nanThe thing is, none of those looks like a bad bin... Their log2 & spread looks OK... Why ? How to fix it ?