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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.
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.
Filter in DepthOfCoverage 3.3-0
We've been using the DepthOfCoverage tool in our pipeline and noticed that the =>Q30 score per gene provided by GATK is significantly different than the =>Q30 score we calculate ourselves without any filters. On your manual page for DOC, you mention using several filters (although it isn't specified if this applies to all versions of GATK or just the last one):
In your general manual page, you mention there is a parameter for disabling filter (--disable_read_filter, -drf). This doesn't seem to be implemented yet in 3.3-0, seeing as I get an error that the argument isn't defined and the argument isn't showing up in the help page either. Is there another way to disable filters in 3.3-0?