3.11.12. Annotate CNVs Matching Current Sample

This algorithm annotates against variants in the selected source, and filters the results to variants with a sample field that matches the current sample.

Requirements

A variant annotation source to use for annotating variants, with a string field that contains the sample name which should be matched to.

Options

The user must specify the following options:

  • Variant Source: The variant source use as an annotation.

  • Sample Name Field: The field in the variant source to match to the current sample

The user may specify the following options:

  • Minimum similarity coefficient threshold is met: Matching annotation regions selected based on the specified minimum similarity coefficient

  • Current record is completely within annotation record: Matching annotation region selected if the CNV is completely within annotation record

  • Current record completely contains annotation record: Matching annotation region selected if the CNV completely contains the annotation record

  • Match CNV Type: This option will cause the algorithm to match on CNV type.

  • Field of CNV Type: The name of the CNV type field to match on.

  • Include counts of matching CNVs: This option will include counts for each CNV type.

Output

The output includes the columns for the selected source. If multiple features match the variant and sample then the values from the last matching feature are used. If a variant does not have a matching feature the fields will be filled in with missing values.