Potential updates to GATK HaplotypeCaller documentation

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Amit

• March 17, 2021 17:00
• Edited

In the HaplotypeCaller documentation, details for using --annotation/ -A option doesn't provide links/details for annotations like StrandBiasBySample, DepthPerSampleHC, AS_InbreedingCoeff, etc that can be used with it. Also, the documentation for those annotations doesn't clearly state it can be used with --annotation/ -A option in GATK haplotypecaller. I had to spend some time connecting the dots. Thought to share in case it helps improving the documentation for the same.

 

Best,

Amit

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  Genevieve Brandt (she/her)

  • March 19, 2021 04:33

  Thanks Amit for the feedback! I will follow up with our documentation team to see if we can make any changes. Feel free to also post your advice to other users in this forum so that we know more about the use cases of our users, and other users in the future will not have to do as much searching.

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