BAM file became smaller after merging

Question

[kimmitzka]

Hello all

I merged 3 bam files but the merge one size were quite smaller than before. Does anyone know the reason?

Thanks

My code is

samtools merge output.bam input1.bam input2.bam input3.bam

[Pierre Lindenbaum]

what is the output of

file input1.bam input2.bam input3.bam

?

[kimmitzka]

output.bam here

[GenoMax]

output.bam here

That can't be the output of the command @Pierre asked you to run.

That aside it is possible to have final output BAM files drop in size after operations that change the read order since the data can compress better leading to smaller files.

[kimmitzka]

so could you tell me how to do if I want to merger these files? Thxx

[GenoMax]

Your command looks fine. I assume you are referring to output file being smaller than adding sizes of the three inputs? Are your input BAM files sorted?