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.
Empty VCF file from GATK-Lite UnifiedGenotyper
(There was another question about a similar symptom, but the answer does not appear to apply to what I'm seeing.)
I get an empty VCF file that just contains the header lines. The input VCF file is 1.8Gb, and as far as I can tell the content is OK - it has MAPQ scores, the flags seem reasonable, etc. I've attached a copy of the console output, and the beginning of the input file in SAM format. Let me know if you have any suggestions. Thanks,