How to merge different BAM files?

Question

[jaafari.omid]

Hello dears all,

I have some BAM files from different samples which they have been mapped to the genome reference using bowtie2. Actually now I want to merge these bam files so that the out put will be a single .bam file. I will be so grateful if you can help me in this purpose.

Regards,

Omid

[Medhat]

From google search:
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
Merging Bam Files
How to merge multiple bam files into single bam file
Merging list of bam files with samtools merge

Answer 1

[swbarnes2]

Did you google "merge bam files"? I see a samtools solution and a picardtools solution, can you explain why those don't work for you?

[jaafari.omid]

Yes I did, but just was not sure if it is completely fit with my purpose or not. If we use the option -h, then only one header will be in the final output?

Regards,

Omid

[swbarnes2]

Well, why don't you try one to see how it works?

[jaafari.omid]

Sorry for the late reply. Yes apparently by that option one header will come in the output's header.