Remove false positives
To run the Remove false positive, go to the toolbox:
Toolbox | Remove Variants (
) | Remove false positives (
)
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:
- Variant frequency Checking this box allows to specify the minimum frequency %. Variants that are present below this frequency (calculated as 'count'/'coverage') will be removed.
- Forward/reverse balance Checking this box allows to specify the forward/reverse balance. Variants with a threshold below the specified threshold will be removed. E.g. if you check the forward/reverse balance setting and adjust this parameter to be a value greater than 0 and less than 0.5, it will then be necessary for at least two reads to be supporting the variant in order to pass this filter.
- Average base quality Checking this box allows to specify the minimum average base quality. Variants with an average base quality below the specified threshold will be removed.
Figure 21.2: This wizard step allows you to adjust the parameters for filtering.