Merge Runlevel Bam Files?

Question

[Hmm]

Illumina HiSeq data: My data was run on 2 flowcells on illumina HiSeq data. I have processed the data and at a point where i have flow cell A and B runlevel data merged. Can anyone tell me the command/tool which i can use to merge flowcell A bam to flow cell B bam. My bams are indexed and sorted.

Thanks

Answer 1

[Pablo]

You should use "samtools merge"

Usage: samtools merge out.bam in1.bam in2.bam

For details, here is the man page: http://samtools.sourceforge.net/samtools.shtml

[Hmm]

do people use MergeSamFiles.jar from the picard tools merge files?

[Hmm]

http://picard.sourceforge.net/command-line-overview.shtml#MergeSamFiles