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2 hours ago by

I need to make one large *.bam file from smaller bam samples. I am confused, which samtools function to use - merge or pileup.
As I understood - when doing BWA, defining Read Group with common lane in tSM option is necessary (say @RGtID:${file1}tLB:{file1}tPL:IlluminatPU:1tSM:${lane})

I only now a bit about samtools merge function; however further I am going to use VarScan for variant calling. And in manual it is written that pileup files are needed for VarScan.
Can I do VarScan tool with merged bam files?
What is the difference between piling and merging with Samtools?
Thank you!

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