I've sequenced targeted DNA panel. I'm aligning it using bwa mem once to the whole genome and twice to the targeted sequences. When aligning it to the reference genome I'm getting ~30% of the reads mapped to the targeted regions. However, when aligning it to the panel sequences 70% of the read are aligned successfully.
Any idea how can it happen? even if there is favored alignment in the whole genome these reads should be assigned as supplementary alignment? Isn't it?