I am using BWA for aligning targeted 'gene-pooled' exonic gene regions generated from Illumina 1.9 against whole genome human reference. The parameters I used for the command "aln" are
bwa aln -n 2 -q 15 -l 35 -t 8 -I
But I was just wondering if it is a good idea to disable the seeding and also change -n to 0.01 ? Also, my sequencing data is Illumina paired-end data (2x250 bp). So will other algorithms such bwa-mem or SMALT be better to use than bwa-aln ?