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