Question: The importance of LB field in @RG tag for BreakDancer analysis
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gravatar for Nicola Casiraghi
3.0 years ago by
Trento, IT
Nicola Casiraghi420 wrote:

I have WGS paired-end data and I want to use BreakDancer to call structural variants. 

Both my case and controls bam files do not have, in their header, the LB field in @RG tag and BreakDancer reports this lack. I can re-header bam files and add the missing LB easily, however I cannot understand how this information is important for BreakDancer and which are the recommended criteria to add them, i.e. a unique LB for all samples or specific for each of them? Is it referred to the Library Preparation Kit?

Could you provide me some hints to solve the problem? Thank you.

breakdancer @rg lb wgs • 1.5k views
ADD COMMENTlink modified 2.9 years ago by Devon Ryan70k • written 3.0 years ago by Nicola Casiraghi420
2
gravatar for Devon Ryan
2.9 years ago by
Devon Ryan70k
Freiburg, Germany
Devon Ryan70k wrote:

Just use picard's AddOrReplaceReadGroups tool to replace the read groups. Assuming that each sample was sequenced only once, just set the library (LB) field to be the same as the sample (SM). So java -jar AddOrReplaceReadGroups.jar I=original.bam O=new.bam SM=sample1 LB=sample1 ....

ADD COMMENTlink written 2.9 years ago by Devon Ryan70k
1
gravatar for Istvan Albert
3.0 years ago by
Istvan Albert ♦♦ 73k
University Park, USA
Istvan Albert ♦♦ 73k wrote:

The LB field is used to identify molecular duplication issues and other sequencing imbalances. For example if the same library is sequenced on different lanes some tools can use this to identify sequencing related artifacts.
 

ADD COMMENTlink written 3.0 years ago by Istvan Albert ♦♦ 73k

Thank you Istvan.

ADD REPLYlink written 3.0 years ago by Nicola Casiraghi420
1
gravatar for ernfrid
3.0 years ago by
ernfrid180
United States
ernfrid180 wrote:

I believe BreakDancer uses the LB tag in two major ways:

  1. To maintain information about that library's insert size distribution. Differences between independent library preparations can intentionally or unintentionally occur and you'll get optimal SV calling by indicating to the software that there are different libraries present.
  2. To increase confidence in a call. SV supporting reads from different libraries increase the score.
ADD COMMENTlink written 3.0 years ago by ernfrid180

Thank you.  However I am still quite confused about the problem. The LB tag is somehow referred to the Library Preparation kit? Could you show me an example of a valid LB tag exploited by BreakDancer? Many thanks again.

ADD REPLYlink written 2.9 years ago by Nicola Casiraghi420
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