When we have two libraries in a bam Samtools does not provide stats on each library so we only have SM level stats but can't push to the individual LB in the LIMS. One option would be to run markdup on each library, then merge the multiple libraries so you could get stats on each LB like we will do for each PU in the planned PCR-free workflow. Alternatively, hopefully the samtools developers will address this limitation (https://github.com/samtools/samtools/issues/1143)
When we have two libraries in a bam Samtools does not provide stats on each library so we only have SM level stats but can't push to the individual LB in the LIMS. One option would be to run markdup on each library, then merge the multiple libraries so you could get stats on each LB like we will do for each PU in the planned PCR-free workflow. Alternatively, hopefully the samtools developers will address this limitation (https://github.com/samtools/samtools/issues/1143)