1. Getting Started
2. Tutorials
3. (How to) Filter variants either with VQSR or by hard-filtering

As mentioned by @stl23, example commands as currently given above require updating to account for syntax change, see https://gatk.broadinstitute.org/hc/en-us/articles/360035532192

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• Matthew Galbraith
• February 07, 2023 00:38
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1. Technical Documentation
2. Troubleshooting GATK4 Issues
3. Known Issues with VariantRecalibrator

Looks like this update has not made it through to https://gatk.broadinstitute.org/hc/en-us/articles/360035531112--How-to-Filter-variants-either-with-VQSR-or-by-hard-filtering

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• Matthew Galbraith
• February 07, 2023 00:35
• 0 votes