I am trying to detect deletions approximately 66bp in length by mapping 90 base reads to the human genome with BWA (and using GATK). By fine tuning the alignment parameters I have managed to increase my maximum detected indel length to around 30 bases but so far I have been unable to improve on that. I have increased the maximum number of gap extensions to 200 and reduced the gap extension penalty to zero so in my head at least, I thought the larger indels would be detectable. Can anyone offer any insight?
Thanks in advance.