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
bwa won't coordinate-sort for you. It's possible that the default output order matches the input. One would just need to compare an input and output to see. If it doesn't and Lina F needs that, then bowtie2 with the
--reorder
option will work.I apologize for any mistaken assumption.
No worries, lh3 just replied anyway and he's obviously the definitive source on this sort of thing :)