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.
BQSR and MD fields
The GATK indel realigner appears to not write an MD field in realigned BAM file entries. I wonder how the base quality score recalibration
program deals with these entries. Does it consider them to be ambiguous and so ignore them, or does it use include them, using the
reference sequence to identify SNPs?