I'm trying to use bwa mem for the first time and I wonder, is it possible to run it on a bam file instead of a fastq file? I noticed that bwa aln can be runned on bam file using '-b' but this option is invalid for bwa mem. The manual does not mention whether it is possible or not. I tried to simply run bwa mem on bam file and the output seems to be a header only sam file.
Does anyone has experience on the question?
Thanks in advance.