GATK for bacteria
The https://github.com/broadinstitute/GATK-for-Microbes Github repository hasn't been updated in a few years and the status is marked as 'alpha'. Is this still the recommended pipeline for bacteria SNP+indel calling?
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Hi SdB
Yes, that is unfortunately the latest and greatest. The funding source we used for that work ran out so we haven't been able to continue it. Everything should still work with the latest GATK though.
-Laura
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