Question: Breakdancer: bam2cfg.pl error
0
gravatar for Peter
3.2 years ago by
Peter0
China
Peter0 wrote:

breakdancer version: 1.4.5

 

${breakdancer}/bam2cfg.pl -g -h ${datindir}/${case} ${datindir}/${control} > output/${s}.cfg

 

Use of uninitialized value $lib in hash element at bam2cfg.pl line 79, <$bam> line 27.

breakdancer • 1.2k views
ADD COMMENTlink modified 3.1 years ago by ernfrid190 • written 3.2 years ago by Peter0
1
gravatar for ernfrid
3.1 years ago by
ernfrid190
United States
ernfrid190 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 3.1 years ago by ernfrid190

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

ADD REPLYlink written 23 months ago by Pawel Osipowski20
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