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.
How to call SNP without confidence SNP ？
I have WGS data of 100 samples. There's few people work on my species,so I didn't find confidence SNP set to use.
I follow the best-practices of GATK. And my question is how to get convinced SNP from my data ? For I see there is a --db snp in the tool HaplotypeCaller.
By the way, someone told me I can call variants by different software and take the same part as my known sites. Does it work?