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How to merge different BAM files?

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

snp next-gen alignment bam samtools
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updated by swbarnes2 swbarnes2 • written by jaafari.omid jaafari.omid

1 answer

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?

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written by swbarnes2 swbarnes2

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

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written by jaafari.omid jaafari.omid

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

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written by swbarnes2 swbarnes2

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

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written by jaafari.omid jaafari.omid

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