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.
vcf / GVCF result sets differ
It seems that running HaplotypeCaller with -ERC GVCF and then running GenotypeGVCFs -stand_call_conf 30 -stand_emit_conf 30 gives a different vcf than HaplotypeCaller -stand_call_conf 30 -stand_emit_conf 30 (on a single sample). Is that expected? I tried versions 3.2 and 3.5.
Tag along question: I've tried to be a good citizen and post questions on existing topics in this forum (instead of starting yet a duplicate thread) but these never get answered. Is it always better to post a new question?
Thanks for your help.