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!
Best practices for joint genotyping of a very large sample size
We are going to variant call 25k+ WGS samples soon. We want to adopt the joint genotyping pipeline provided at https://github.com/gatk-workflows/gatk4-germline-snps-indels/blob/master/joint-discovery-gatk4-local.wdl & https://github.com/gatk-workflows/gatk4-germline-snps-indels/blob/master/joint-discovery-gatk4-local.hg38.wgs.inputs.json.
1. One problem is that this pipeline uses a gvcf file, and gvcf is much bigger than vcf in size. So I am not sure if it is practical to have a gvcf file for 25k+ samples.
2. Another problem is memory usage. Can we joint genotype 25k+ WGS samples at once?
The above being said, I am wondering if we could divide the 25k+ samples into smaller groups (e.g. 1000 samples each group), do joint genotyping group by group, without compromising variant calling quality too much. By dividing, we should save space, memory, and time.
BTW, where can I find the gvcfs such as "/home/bshifaw/data/joint_discovery/NA12878.g.vcf.gz" and ""/home/bshifaw/data/joint_discovery/NA12878.g.vcf.gz.tbi"?