I have dataset which is exome-seq, and I am planing to use bwa aln for alignment with its default values, and use the GATK for indel / snp information. I checked the bwa manual which didn't show anything about indel size. If I set the -n value 2 mismatch, then lot of my reads with larger indel size > 2 will not be able to map on the reference genome. I heard the parameter bwa mem doesn't have this limitation and it can handled a larger indel size.
Thanks in advance!