When running breakdancer bam2cfg.pl I get the following error.
breakDancer_1.4.1/breakdancer/perl/bam2cfg.pl -C input_dedup_realigned.bam Coefficient of variation 4.61403040060899 in library lib_ACI is larger than the cutoff 1, poor quality data, excluding from further analysis.
When I increase the coefficient of variant cutof to 5 I get the following insert size numbers / cutoffs.
breakDancer_1.4.1/breakdancer/perl/bam2cfg.pl -C -v 5 input_dedup_realigned.bam lower:0.00 upper:275514842.99 mean:3215555.46 std:14836670.63 SWnormality:-74.09
These are of course not very useful.
On the exact same bam our inhouse tool gives the following mean and cutoffs
insertCutoff: 42 mean: 113 deletionCutoff: 253
Delly from the EMBL also gives the following median and deletionCutoff.
Median: 154 insert size cutoff: 279
Why do I get the strange insert size cutoffs with breakdancer bam2cfg? Doesn't it exclude outliers in the data ?