Hi all,

I was wondering if the order of records in a bamfile produced by bwa aln/mem/sampe is guaranteed to be the same as in the fastq files that were used as input.

I checked the bwa manual but the only thing I found is this: "Repetitive read pairs will be placed randomly" (part of sampe description).

If anyone has an idea, I'd welcome your feedback!

Best,  
~Lina
Yes, the same.