How does Genomicsdbimport for polyploids work?

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Homa Papoli

• October 25, 2021 08:57

Hello,

In the documentation for Genomicsdbimport it is stated that the tool is designed for diploids. I used it, however, for my tetraploid (4n) samples, it ran successfully. I then used the outputs for GenotypeGVCF and this tool is also producing the VCF files successfully.

I was wondering, given the successful run, can I trust the output or should I be worried for errors in my output since Genomicsdbimport is designed for diploids?

I'm using GATK version GATK/4.1.4.1

Thank you,

Homa

 

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  Pamela Bretscher

  • October 25, 2021 13:40

  Hi Homa Papoli,

  I believe the note about diploids is only present in the GenomicsDBImport documentation for much older versions of GATK, but this is no longer a limitation. In the current documentation, it is not stated that the tool is limited to diploids, as this has been addressed in newer versions of GATK. This is why the tools are running properly for you, and I don't think you should see any issues as a result of ploidy. 

  Kind regards,

  Pamela

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  Homa Papoli

  • October 25, 2021 14:03

  Thank you very much, indeed, all results seem absolutely fine. Thanks again!

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