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.
quality score error
Hi I am using whole genome sequence data of sanger sequencing, and I am having the error:
we encountered an extremely high quality score of 68
One posible solution is to use the flag -allowPotentiallyMisencodedQuals
The only explanation about this flag that I found is: Ignore warnings about base quality score encoding, and is here https://wiki.gacrc.uga.edu/wiki/Gatk
Thus if I use this flag I can conserve this "High quality score" bases for the analysis and SNP calling? Because that is what I want.
Thank you very much