I have been reviewing some of my call data from a recent large exome run and after reviewing heterozygous calls made by HaplotypeCaller, I decided to confirm the base change in my recalibrated bam files. However when I viewed the bam files I discovered that many of the base pair quality were quite low. This left me puzzled as to why HaplotypeCaller would call this het. I also review the command line options and found that --min_base_quality_score is defaulted to 10, which also seems low. Is their a reason for this default (downstream), that I'm unaware of.
My genotype for this individual is: HLHS0007 0/1 72,14 86 99 126,0,4289
The recorded change chr16:74951843 T->C
And I've attached the images of my tview alignments at this position as well.
Thanks for your insight.