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.
reads used for variant calling
I have pair-end sequencing data. If read1 is mapping uniquely, read 2 is mapped to multiple locations equally. And read1 and read2 are proper mapped (within the fragment size range, and the strands are also OK (head to head)). Will these reads be used in variant calling (HaplotypeCaller and UnifiedGenotyper)?