HaplotypeCaller not catching variants
I am currently having an issue where HaplotypeCaller is not catching at least one specific variant. I have searched forums and have used the -bamout option as suggested by some. While the bam file output from this appears to be much different than the bam file generated from my BQSR step, it still shows the variant 10% of 220 reads with an average quality of 30.1; the BQSR bam shows 57% of 310 reads with average quality of 30.8.
I have run UnifiedGenotyper on this same interval and that picked up the variant. I am very confused as to why this variant is not picked up.
I do not understand why one is able to pick it up and the other is not. It is important that this variant be found because this is a control sample, and is showing as a somatic mutation when compared to its affected sample when in fact it is a germline mutation.
Does anyone have any suggestions?