Remove false positives

To run the Remove false positive, go to the toolbox:

        Toolbox | Remove Variants (Image remove_information_closed_16_n_p) | Remove false positives (Image gg_filter_frequency)

This tool will remove false positives by removing variants with low frequency, low average quality, and a bad forward/reverse balance.

After you have selected the variant track that you would like to remove false positives from, you can adjust the filter parameters to specify how many reads should be supporting a variant to pass the filter (figure 21.2).

The Filter options are:

Image remove_false_positives_step3
Figure 21.2: This wizard step allows you to adjust the parameters for filtering.