Filter by alignment

The Alignment screen is the one of several screens for filtering a multi-sample Variants view or set, and lets you filter variants in the Variants view based on alignment statistics.

Put a check mark next to each type of statistic you wish to filter on, then input a minimum and/or maximum threshold for that setting.

• P not ref – The probability that the called base at this position is not the reference base.

• Q call – The Phred-like quality score of the called genotype; a measure of the probability that the called genotype is correct.

• SNPs – The Minimum and Maximum percentage of reads that should contain a variant at a given position.

• Depth – The minimum depth of reads needed to include the variant.

Once you have made your selections, do any of the following:

• To select additional filtering options in the wizard, click Experiment, Type, Impact, or Database on the left of the wizard. If you are filtering a variant set, you can also click Name to overwrite the default name and notes for the set.

• To apply the screen options and keep the wizard open, click Apply. Note: Once you press Apply, the button becomes temporarily disabled. When you make further changes to the filter, the button is once again enabled.

• To apply the screen options and close the wizard, click OK.