Breakdancer: bam2cfg.pl error

Question

[Peter]

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.

Answer 1

[ernfrid]

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.

[Pawel Osipowski]

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