How do I use different intervals with GenomicsDBImport?

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Ahmed S. Chakroun

• April 11, 2021 12:53
• Edited

Hi,

I have 3 exome data callsets produced using different capture kits with different intervals lists, say: kit-1, kit-2 and kit-3 and I would like to check if the commands below are still consistent with the best practices:

gatk --java-options "-Xmx4g -Xms4g" GenomicsDBImport \
     --genomicsdb-workspace-path myDatabase \
     -L kit-1_intervals.bed \
     -L kit-2_intervals.bed \
     --merge-input-intervals \
     -V sample-1_kit-1.g.vcf.gz \
     -V sample-2_kit-1.g.vcf.gz \
     -V sample-1_kit-2.g.vcf.gz \
     -V sample-2_kit-2.g.vcf.gz

and

gatk --java-options "-Xmx4g -Xms4g" GenomicsDBImport \
     -V sample-1_kit-3.g.vcf.gz \
     -V sample-2_kit-3.g.vcf.gz \
     -L kit-3_intervals.bed \
     --merge-input-intervals \
     --genomicsdb-update-workspace-path myDatabase

Thanks for help.
Regards

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• 

  Genevieve Brandt (she/her)

  • April 22, 2021 22:26

  Ahmed S. Chakroun the --genomicsdb-update-workspace-path can only be used to add more samples, not more intervals. You must use the same intervals that are originally used. More information can be found in the Tool Docs: https://gatk.broadinstitute.org/hc/en-us/articles/360057439331-GenomicsDBImport

  Best,

  Genevieve

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  Ahmed S. Chakroun

  • April 22, 2021 22:45

  So, it's not recommended to mix exome data captured using different kits (say Agilent SureSelect V6 and V7) within the same GenomicsDB, isn't it?

  Thank you very much for your help.
  Kind regards.

  Ahmed

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  Genevieve Brandt (she/her)

  • April 22, 2021 22:53

  Depends on your research, here is more information about how GATK uses intervals. The GATK engine will merge overlapping intervals.

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