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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.
what is defined as a candidate region in haplotypecaller?
I learn that HaplotypeCaller looks for candidate regions and builds a denovo assembly. So how is this region defined? How big is the region?
Recently we found a six base pair insertion in an interesting gene using HaplotypeCaller which UnifiedGenotyper missed. We sanger sequenced it and found it to be true. Happy!!! But when I tried to write a bam file with bamout option using a 1MB flanking window and the alignment looked totally new and the variant disappeared. In fact there were no reads covering that position in the new assembly.