Remove Marginal Variants

Variant calling is always a balance between sensitivity and specificity. Remove Marginal Variants is designed for the removal of potential false positive variants. The tool can be configured to remove variant calls with low frequency, a skewed forward-reverse reads balance, or those predominantly supported by low quality bases.

A new variant track is produced as output, leaving the original variant track as it was.

To run Remove Marginal Variants, go to:

        Toolbox | Resequencing Analysis (Image resequencing) | Variant Filtering (Image variant_filtering_folder_closed_16_h_p) | Remove Marginal Variants (Image filter_frequency_16_n_p)

This opens a dialog where you can select a variant track (Image variant_track_16_n_p).

Click on Next to move to the dialog where filtering thresholds can be set, as shown in figure 29.2.

Image filter_marginal_variant_calls_step3
Figure 29.2: One or more thresholds can be configured, defining the basis for variant removal.

The following thresholds can be specified. All alleles are investigated separately.

If several thresholds are applied, just one needs to be fulfilled to discard the allele. For more information about how these values are calculated, please refer to Variant tracks.

If all non-reference alleles at a position are removed, any remaining homozygous reference alleles will also be removed at that position.

A new variant track is produced by this tool, containing just the variants that exceeded the configured thresholds.