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.

info about small_exac_common_3.vcf.gz

I am using small_exac_common_3.vcf.gz to estimate contamination and I would like to know a few details on what are the filters of that file and what's the source. To be more specific:
1. How many common bi-allelec sites, there are?
2. What's the source of the file?
3. Does it include specific sites? hom, het, all sites from all chr?
4. Does it include extra contigs?
4. are there any filters about AF?
5. Any other filters?

I would appreciate any feedback and guidance.


Sign In or Register to comment.