Running the variant caller on a case and control sample separately and filtering away variants found in the control data set gives not in all cases a satisfactory result as many variants in the control sample have not been called. This is often due to lack of read coverage in the corresponding regions or too stringent parameter settings. Therefore, instead of calling variants in the control sample, the Filter against control reads tool should be used to remove variants found in both samples from the set of candidate variants identified in the case sample.
Toolbox | Resequencing () | Compare Variants | Filter against Control Reads
The variant track from the case sample should be used as input and when you click Next you will need to provide the read track from the control data set (see figure 26.27).
When clicking Next, you are asked to supply the number of reads in the control data set that should support the variant allele in order to include it as a match. All the variants where at least this number of control reads show the particular allele will be filtered away in the result track.
Please note that variants, which have no coverage in the mapped control reads will be reported too. You can identify them by looking for a 0 value in the column 'Control coverage'.
The following annotations will be added to each variant not found in the control data set:
- Control count
- For each allele the number of reads supporting the allele.
- Control coverage
- Read coverage in the control dataset for the position in which the allele has been identified in the case dataset.
- Control frequency
- Percentage of reads supporting the allele in the control sample.