Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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 for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

How to get a smaller list of deNovo SNPs between 3 genotype

Hello. I am currently working on maize whole genome dataset and I have 3 samples- WT, MT and B73. I obtained the VCF files for all 3 datasets using the haplotype caller. However, the list of SNPs that I am getting on comparing these 3 samples on just chromosome 3 is more than 200,000. Is there any way, I can get a shorter and more complied list of de Novo SNPs which I could possibly work on?
I also had another question related to creating the .ped file for my 3 samples of maize. Is there anyway that I can create a .ped file for maize samples as I want to do a trio analysis on the same samples and what are the tools that I can use to create this file. Thank you.


Sign In or Register to comment.