Identify Shared Variants

This tool should be used if you are interested in finding common (frequent) variants in a group of samples. For example one use case could be that you have 50 unrelated individuals with the same disease and would like to identify variants that are present in at least 70% of all individuals. It can also be used to do an overall comparison between samples (a frequency threshold of 0% will report all alleles).

        Toolbox | Resequencing Analysis (Image resequencing) | Variants Comparison (Image variant_compare_folder_closed_16_h_p) | Identify Shared Variants (Image common_variations_16_n_p)

This opens a dialog where you can select the variant tracks (Image variant_track_16_n_p) from the samples in the group.

Clicking Next will display the dialog shown in figure 32.9.

Image compare_variants_within_group_step2
Figure 32.9: Frequency treshold.

The Frequency threshold is the percentage of samples that have this variant. Setting it to 70% means that at least 70% of the samples selected as input have to contain a given variant for it to be reported in the output.

The output of the analysis is a track with all the variants that passed the frequency thresholds and with additional reporting of:

Note that this tool can be used for merging all variants from a number of variant tracks into one track by setting the frequency threshold to 0.