Annotate Variants with Unique Molecular Index Info

The tool Annotate Variants with Unique Molecular Index Info annotates the variants with UMI groups information generated by the Calculate Unique Molecular Index Groups, and produces the annotated variant track as output.

The tool can be found in the Toolbox here:

        Tools | QIAseq Panel Expert Tools (Image qiaseq_expert_folder_closed_16_n_p) | QIAseq DNA Panel Expert Tools (Image qiaseqv3_folder_open_16_h_p) | Annotate Variants with Unique Molecular Index Info (Image annotate_var_bc_16_h_p)

In the first dialog (figure 5.53), select a variant track.

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Figure 5.53: Select a variant track.

In the second dialog, select a read mapping. The tool works on any read mapping on which UMI groups have been calculated, i.e. a read mapping consisting of raw reads or a read mapping consisting of UMI consensus reads generated by the Create UMI Reads from Grouped Reads tool (as seen on figure 5.54). If the read mapping consists of UMI reads, check the "Mapping consists of UMI reads" option.

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Figure 5.54: Select a read mapping.

The parameters below are used to calculate the annotations:

Finally, it is possible to filter the data using the following options:

Annotations

The following annotations are added to the variants found using a read mapping consisting of raw reads, while only the three annotations indicated with a * are added when the read mapping consists of UMI reads. When using the Analyze QIAseq DNA Panels guide or the Identify QIAseq DNA Variants workflow, the annotations are always based on UMI reads.

The annotations differ when the tool is used with UMI reads as it is not possible to calculate annotations involving how many reads in a read group have the variant from the UMI consensus reads. This is for example "Found matching groups with good part matching", "Found matching groups by reads and group sizes", etc.. These columns then assume that all reads in a read group have the variant, that means that all matching UMI groups are Consistent. It is also not possible to calculate how many reads match a variant and how many do not. Many columns show a frequency of reads and also a frequency of groups, e.g. "Found matches" and "Found matches UMI-groups". When running on UMI reads, these two numbers will be the same.