Sample Does Not Contain Any Normals

Question

[roalva1]

Hello,

I am calling BreakDancer and I don't get any result. This is the output file #Software: 1.3.7-unstable-6-071043d #Command: /clinicfs/projects/naranjoma/pipeline/code//breakdancer/breakdancer-max sample2.cfg #Library Statistics: sample does not contain any normals #sample2.bam mean:458.89 std:44.74 uppercutoff:617.71 lowercutoff:258.75 readlen:100 library:sample reflen:1999810 seqcov:92.9764 phycov:213.33 1:253 2:21319 3:3977 4:8128:208 32:3552 #Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type Size Score num_Reads num_Reads_lib sample2.bam Max Kahan error: 0

And I see this Max Kahan Error and sample does not contain any normals While my config file is quite normal. readgroup:sample platform:illumina map:sample2.bam readlen:100.00 lib:sample num:10001 lower:258.75 upper:617.71 mean:458.89 std:44.74 SWnormality:-54.06 exe:samtools view

I have used the same command with other samples and everthing went ok. any idea?

Best regards

Answer 1

[roalva1]

I've found the problem. Read names where finish like this:

HWI-ST700660:1:2102:9367:69695#ATCACGA

instead of

HWI-ST700660:1:2102:9367:69695#0/1

So breakdancer was unable to find out anything. Some others softwares like delly are able to do that, and also this ATCACGA thing is standard and in a lot of illumina reads. I would suggest Ken Chen to support this kind of reads.

Best Regards