Toolbox | Resequencing () | Annotate and Filter | Filter Marginal Variant Calls
This opens a dialog where you can select a variant track () with experimental data that should be filtered.
Click Next to set the filtering thresholds as shown in figure 25.54
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.
- Variant frequency
- The frequency filter will remove all variants having alleles with a frequency (= number of reads supporting the allele/number of all reads) lower than the given threshold.
- Forward/reverse balance
- The forward/reverse balance filter will remove all variants having alleles with a forward/reverse balance of less than the given threshold.
- Average base quality
- The average base quality filter will remove all variants having alleles with an average base quality of less than the given threshold.
The result is a new track where all variants (or at least one non-reference allele of the variant) fulfill the criteria.