[Breakdancer-help] problem with bam2cfg

[Brown, S. <Stu...@ny...>]

I am trying out BreakDancer for the first time, using a set of Paired-End Illumina data from NCBI/SRA. We have plans to use this for a major translocation project starting soon.

I first aligned to Reference genome with bwa, now trying to build BreakDancer config file with bam2cfg.pl

I get this error message:

[genomes@hactar perl]$ perl bam2cfg.pl -g /projects/BreakDancer/Mouse_mm9_fa/Mouse_aln.sort.JH.bam
Use of uninitialized value in printf at bam2cfg.pl line 224.
readgroup:NA	platform:illumina	map:/projects/BreakDancer/Mouse_mm9_fa/Mouse_aln.sort.JH.bam	readlen:31.00	lib:NA	num:10001	lower:80.16	upper:564.72	mean:403.89	std:59.70	SWnormality:-72.01	flag:0	exe:samtools view


Any ideas what this means and how to fix?


Thanks

Stuart Brown
stu...@ny...





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