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Pileup or merge?

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!

rna-seq
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written by storm1907 • storm1907

What is the difference between piling and merging with Samtools?

Have you read the help information? Have you generated pileup files and looked at them?

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written by swbarnes2 swbarnes2

Not at the moment, Im out of time. I am going to merge the files, but I also want to use Varscan

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written by storm1907 • storm1907

Edit ::: Now deleted by OP.

Hello storm1907!

We believe that this post does not fit the main topic of this site.

With respect, it is expected that you invest at least the effort of reading the documentation of tools you use. Saying you are out of time but then posting a question implies that your time is more valuable of those of the community members who you expect to do your work.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by ATpoint ATpoint

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