Closed bogdang989 closed 6 years ago
Split input BAM/SAM/CRAM into BAM per RG.
Use Samtools split for this purpose.
Picard RevertSam time 4h 7m Samtools Split time 28m
/opt/samtools-1.7/samtools split -f '%!.bam' -@ 29 ae3b4fcd963d404081393b9cf038d4d5.bam
Samtools split is tested with a randomly selected BAM from the pilot set. QualityYield metrics show that there is no difference in tool outputs, which is expected since it is a simple tool.
Tools in the workflow
Current function
Split input BAM/SAM/CRAM into BAM per RG.
Proposed modification
Use Samtools split for this purpose.
Performance improvement
Picard RevertSam time 4h 7m Samtools Split time 28m
Example command line
Samtools split is tested with a randomly selected BAM from the pilot set. QualityYield metrics show that there is no difference in tool outputs, which is expected since it is a simple tool.