Question

How to merge different BAM files?

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4.5 years ago

jaafari.omid ▴ 80

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 • 3.0k views

ADD COMMENT • link updated 4.5 years ago by swbarnes2 14k • written 4.5 years ago by jaafari.omid ▴ 80

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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

ADD REPLY • link 4.5 years ago by Medhat 9.7k

score 0 · Answer 1 · 2019-10-08

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4.5 years ago

swbarnes2 14k

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?

ADD COMMENT • link 4.5 years ago by swbarnes2 14k

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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

ADD REPLY • link 4.5 years ago by jaafari.omid ▴ 80

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

ADD REPLY • link 4.5 years ago by swbarnes2 14k

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

ADD REPLY • link 4.5 years ago by jaafari.omid ▴ 80