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.
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.
I am working in a exome sequencing project in family trios. I have used all the Best Practices to analyze the sequences. I ran the PhaceByTransmission walker with the ‘’MendelianViolationsFile flag hoping that the generated Mendel violation filed would give me information about the possible de novo variants. Nonetheless, I did not understand what the columns of the output file mean. Could you please help me to understand the file’s nomenclature?
I also tried to extract the de novo variants using an in house script but I am not sure about the nomenclature of the phased .vcf file. I would like to know the difference between ./. , 1/0, 0/1 and 1/1 among the three family members. For example, I obtained 0/1 ./. ./. (for child, mother, father) but I do not know if I extract this row, this might represent a de novo variant.
Thank you for your time