Remove Marginal Variants

Variant calling is always a balance between sensitivity and specificity. To get rid of potential false positive variants, you can use this tool on a variant track to remove some of the variant calls, which are supported by only low quality bases, have low frequency or a skewed forward-reverse reads balance. In this way, you can try different strategies for filtering without re-running the variant detection.

        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) with experimental data that should be filtered.

Click Next to set the filtering thresholds as shown in figure 29.2

Image filter_marginal_variant_calls_step3
Figure 29.2: Specifying thresholds for filtering.

The following thresholds can be specified. All alleles except the reference allele are investigated separately, but in order to remove a variant, all non-reference alleles have to fulfill the requirements.

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.

The result is a new track where all variants (or at least one non-reference allele of the variant) fulfill the criteria.