Using this software0. For impatient users
1. Data inputs
2. Create a project
3. Annotate a project
Using user annotation track
4. Filter for quality scores
5. Main user interface
6. SVA genome browser
7. SVA tables
8. Selecting genes or regions
Bio-pathway or GO
Fisher's exact test
10. Exome or targeted capture sequencing
Filtering for variant quality scores
SVA provides a number of filter tools, including a quality score (confidence score) filter for each type of variants (see figure below).
There are two strategies in filtering for variant quality score:
1. Set the quality filtering criteria
The quality filtering criteria can be set through the strategy 1 menu items (figure above) or buttons (figure below). The menu items and the buttons do exactly the same things.
I will use the quality filtering for single nucleotide variants (SNVs) as an example of this process. Click on either the menu item or the button, you will see a window like this:
In this example for SNVs, we have six different scores to potentially use as quality filter: (Phred-like) concensus score, SNP quality, RMS score, read depth, reads supporting SNV, reads supporting the reference base.
We used these thresholds for SNVs:
I listed these thresholds here for your reference. You can certainly consider and set your confidence score thresholds.
After you click on the "FILTER" button, the SNV, INDEL, and CV listing tables will be automatically updated. A status bar at the bottom of the window will update you how many in total and how many remain after the filtering (figure below). In this example below, the status bar indicates the "Score " (filtering) is "on ". And the number of filtered count is 333789 - equal to the total. This is because in the chromosome-X example dataset released with SVA, the dataset has been individually filtered with strategy 2.
The strategy 1 filter will apply to most of the variant analysis and summarization procedures in SVA. In fact when you perform any variant analysis and summarization procedures, please pay attention to the output printed onto the "Log" panel: . Any filters applied in the procedures will be printed there - and if you do not see a specific filter is "on", then that filter is not applied.
When you load the project, you also have an option to automatically apply a default quality filter (figure below). If you dislike the default one, you can simply reset it and apply a new one after the project is loaded.
Lastly, please note that the thresholds set here will also be applied to strategy 2, if you want to individually filter the variants and export to a new project - i.e., although the figure above does indicate "average scores", the thresholds are actually the same for strategy 2 - but the filtering process will be different.
2. Perform strategy 2 filtering
Click on menu "Filter -> Individual variant confidence score filtering and exporting", you will be asked to export the filtered dataset to a new project.
3. reset the quality filtering criteria
You may reset the quality filter (with all other filters) by clicking on menu "Filter -> Reset all filters".
© 2011 Dongliang Ge, PhD.