Question About Bwa Aln Handled The Indel Size

Question

[ge.yunqing90]

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!

Ge

Answer 1

[swbarnes2]

I've seen bwa correctly map a read with a 10 base pair deletion, but it was only able to do this because the mapping position of the mate kicked on the Smith-Waterman mapping for that read.