Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.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.

Trio analysis using the GATK toolbox

alphahmedalphahmed JAPANMember
edited March 2017 in Ask the GATK team

While I am following the Best Practices documents, I started to get confused about the best sequence of steps to follow, after calling the common VCF file of the child, and parents. Some steps seem not applicable to a total WGS sample of three; like variant-recalibration. Meanwhile, variant recalibration is essential to reduce FPs, and increasing specificity before going any further with analysis.

Although I do understand that tools like PhaseByTransmission, and Genotype Refinement work-flow, are among the most discussed ones, I wonder if there is any "Best Practices" or "Documentation" section that specifically addresses Trio Analysis? Especially with all the additions to the new GATK version.

Thanks in advance for the help.

Best Answer

Answers

Sign In or Register to comment.