Closed:Pileup or merge?
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8 months ago
storm1907 • 0

Hello, 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 @RG\tID:${file1}\tLB:{file1}\tPL:Illumina\tPU:1\tSM:${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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