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Old 01-06-2012, 08:34 AM   #1
Location: Pittsburgh

Join Date: Aug 2011
Posts: 72
Unhappy merging many bam files-novice needs help please

I have 152 coordinate sorted bam files. I want to merge them. I have tried both Samtools merge and Picard. I used Samtools merge before on some different data and it worked but I don't think that data was coordinate sorted and that might make a difference. The command I am trying to use is

samtools merge /out.bam /path_to_file/*.bam

I want it to merge all the files in that folder. I don't get a specific error but it prints out the samtools merge usage parameters. So I guess I am missing something in my command. The following is what I have done so far in my pipeline:

1. aligned with bowtie 2 (output sam)
2. sorted individual sam files output to individual bam files

The end goal is to use GATK for variant analysis. According to, I need to put some kind of -r argument in Samtools when I am processing to add an @rq (or something like that).

I am lost at this moment and I have searched and searched to try and find an answer on the forums.
shawpa is offline   Reply With Quote
Old 01-06-2012, 08:51 AM   #2
Junior Member
Location: Montreal

Join Date: Sep 2011
Posts: 6

Hi Shawpa,
As an aside, you don't need to merge the bam files when calling the UnifiedGenotyper, you can use multiple -I parameters. Note that you can expect compute time to increase in a non-linear fashion when doing this.
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Old 01-06-2012, 09:03 AM   #3
David Eccles (gringer)
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 838

Originally Posted by shawpa View Post
samtools merge /out.bam /path_to_file/*.bam
If this is the precise command you used, you may get better results from removing the initita forward slashes.
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