If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
HaplotypeCaller genotype likelihoods
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
And I've attached the images of my tview alignments at this position as well.
Thanks for your insight.