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 November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.
Training data for VQSR step
I want to run VQSR for my Exome data. I have finished with data pre-processing and joint genotyping. Now, I want to move to the next step which is VQSR (still in the first step, VariantRecalibrator). I noticed that I don't have the training set for the tools parameter's input. Where can I download the vcf file that I need to run this command? This is what I've tried:
I tried to open HapMap website and I found allocated SNPs download link. Is this the file I need? The file are in XML format and splitted per chromosome and it based in Hg35. Do I need to join these XML and then convert it to VCF using GATK? Will it give some problem with the different HG build (I use HG38)
I found the VCF file also per chromosome. I think I just need to join it, don't I? probably you can give some suggestion how to join it properly?
I don't know where I can get this file.
I think I already have this file. I have use it during the GATK pre-processing step. It is the same file, right?
Thank you for your help.