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.
--stand_emit_conf and --stand_call_conf setting in Haplotypecaller
I have processed samples using GATK 3.1 Haplotypecaller according to the RNA Seq best practice.
Haplotypecaller is set with --stand_emit_conf = 20 and --stand_call_conf = 20 options, but I could find variants which QUAL less than 20 in the output gVcf file and variants which its QUAL < 20 is not marked as LowQual.
I wonder what those parameters do for Haplotypecaller.
I have run with --stand_emit_conf = 20 and --stand_call_conf = 30 for testing. Output gvcf file appears to be identical.