[Breakdancer-help] problem with bam2cfg
Status: Beta
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From: Brown, S. <Stu...@ny...> - 2010-07-22 13:49:35
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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... ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= |