View Single Post
Old 01-29-2019, 12:39 PM   #4
Senior Member
Location: Québec, Canada

Join Date: Jul 2008
Posts: 260

If you'are using "bwa sampe" for aligning, the documentation says:

Generate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randomly.
I don't know if it is the case with "bwa mem" or with "bwa aln".
seb567 is offline   Reply With Quote