Compare Variants Across Samples

The Compare Variants Across Samples can be used to compare samples originating from strains or species sharing a common reference. The workflow takes trimmed, host-filtered reads as input such as output produced by the Data QC and Remove Background Reads, Type a Known Species, Type Among Multiple Species or Analyze Viral Hybrid Capture Panel Data workflow. As the workflow removes duplicate mapped reads, amplicon data is not recommended as input. However, the workflow can be modified to work on amplicon data by opening a copy of the workflow, removing the Remove Duplicate Mapped Reads tool and saving the modified workflow.

To run the Compare Variants Across Samples workflow, go to

        Toolbox | Template Workflows (Image workflow_group) | Microbial Workflows (Image mgm_folder_closed_flat_16_h_p) | Typing and Epidemiology (Image typing_epi_folder_closed_16_h_p) | Compare Variants Across Samples (Image compare_var_across_16_h_p)

An overview of the workflow can be seen in figure 3.33.

Image compare_var_wf_overview
Figure 3.33: An overview of the Compare Variants Across Samples workflow

Saving the workflow output will generate the files shown in (figure 3.37) and optionally, a workflow result metadata table.

Image compare_var_wf_output
Figure 3.37: Output from Compare Variants Across Samples workflow

The workflow generates outputs for each batch analysis run as well as a folder for each sample. For each sample, the following is output:

Image compare_var_wf_sample_output
Figure 3.38: The track list generated for each sample analysis

For each batch analysis run, the following outputs are generated:

For more information on the tree tools, see Create SNP Tree.