I am posting at the request of a friend at WashU. I am not sure if this issue has been resolved with the latest release. I was following the pipeline described here: http://breakdancer.sourceforge.net/pipeline.html
Using BreakDancer-1.3.6 (at least that's what the readme file says) with the following command lines:
perl bam2cfg.pl -g -h Tumor.bam Normal.bam > breakdancer.cfg
breakdancer-max breakdancer.cfg > breakdancer_SVpred.out
In the output file, it looks like all putative SVs are reported as coming from Normal.bam (column 11), even when I switch the order in the first step. Am I reading the output file incorrectly?
Thanks!
-HC
My .cfg file looks like this:
readgroup:NA platform:illumina map:Tumor.bam readlen:100.00 lib:NA num:10001 lower:69.53 upper:606.49 mean:322.73 std:67.07 SWnormality:-17.32 flag:0 exe:samtools view
readgroup:NA platform:illumina map:Normal.bam readlen:100.00 lib:NA num:10001 lower:60.58 upper:693.63 mean:366.08 std:79.10 SWnormality:-11.69 flag:0 exe:samtools view
My output file looks like:
#Software: 1.3.7-unstable-6-071043d
#Command: bin/breakdancer-max breakdancer.cfg
#Library Statistics:
NA does not contain any normals
#Normal.bam mean:366.08 std:79.1 uppercutoff:693.63 lowercutoff:60.58 readlen:100 library:NA reflen:2951015189 seqcov:0.604493 phycov:1.10646 1:3323 2:19395 3:42 4:9847 8:3523 32:943645<br>
#Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type Size Score num_Reads num_Reads_lib Normal.bam Tumor.bam<br>
chr1 3418549 12+8- chr1 3418616 12+8- ITX -302 99 3 Normal.bam|3 NA NA<br>
chr1 142537742 3+12- chr1 142541128 31+9- ITX 2706 99 2 Normal.bam|2 1191376.25 NA<br>
chr1 210827199 31+59- chr1 210827331 31+59- ITX -297 99 7 Normal.bam|7 NA NA<br>
chr2 89872705 14+109- chr2 89872940 14+109- INV -365 99 2 Normal.bam|2 NA NA<br>
chr2 133017381 746+65- chr2 133018487 5+124- DEL 1226 99 31 Normal.bam|31 231473.78 NA<br>
...<br>
Could you please tell how to extract information to pass on AddOrReplaceReadGroups, either from mapped BAM or Fastq files.