HomeCLC software: Important notificationsIssues affecting only versions of products released prior to June 2017VCF export - updating the "Exclude from enforced diploid" list in Worfklow design - GWB 6.5.1

3.20. VCF export - updating the "Exclude from enforced diploid" list in Worfklow design - GWB 6.5.1

The issue

When designing a Workflow and configuring VCF export functionality in the Genomics Workbench 6.5.1, clicking in the box labeled Enforce diploid does not cause the elements for the Exclude from enforced diploid box to be updated automatically.

The work-around

Work-around one (recommended)

Click on the small icon of a lock beside the Exclude from enforced diploid box. This causes the elements to be updated to reflect your chosen genome.

Clicking on the lock icon twice will set it back to its original state. (By default, for this option, it is locked.)

Work-around two

After choosing your genome and clicking in the box next to Enforce diploid, close the configuration wizard by clicking on the button labeled Finish.  Then double click on the Export VCF element in the Workflow design form again. Doing this will cause the list for the Exclude from enforced diploid element to be updated.

 

Further information

VCF export from the Genomics Workbench version 6.5.1 has been improved by the addition of an option to specify whether the genome in question should be considered diploid. In addition, the option to exclude certain references in the genome from being considered diploid has been added. For example, in the case of mammalian male samples, one would want to specify that chromosomes X, Y and the mitochondrial reference should not be considered diploid.

When calling the VCF export functionality directly, if you check the box labeled Enforce diploid, the list of references in your selected genome is updated, so that if you then check on the plus symbol to the right of the Exclude from enforced diploid box, you see a list of those references to choose from. As of version 7.0 of the Genomics Workbench, released in February, 2014, the Exclude from enforced diploid field should be updated automatically when configuring a Workflow also.

Knowledge Tags
workflow  /  vcf  /  problem  / 

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