Question: Breakdancer: error
gravatar for Peter
5.9 years ago by
Peter0 wrote:

breakdancer version: 1.4.5


${breakdancer}/ -g -h ${datindir}/${case} ${datindir}/${control} > output/${s}.cfg


Use of uninitialized value $lib in hash element at line 79, <$bam> line 27.

breakdancer • 2.2k views
ADD COMMENTlink modified 5.9 years ago by ernfrid210 • written 5.9 years ago by Peter0
gravatar for ernfrid
5.9 years ago by
United States
ernfrid210 wrote:

Your BAM header should have @RG read group entries that indicate the library sequenced (LB:), the sample (SM:), and the ID (ID:). For example:

@RG    ID:someid    PL:illumina    LB:H_IJ-NA19238-NA19238-lib1    SM:H_IJ-NA19238-NA19238

Additionally, library names should be unique across samples.

You should also be aware that BreakDancer expects that each read will be properly tagged indicating the read group is came from. 

ADD COMMENTlink written 5.9 years ago by ernfrid210

... and you can do this by 'bamaddrg' e.g.

ADD REPLYlink written 4.7 years ago by Pawel Osipowski20
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