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 6.87), select a variant track.

Image annotatebarcode
Figure 6.87: 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 6.88). If the read mapping consists of UMI reads, check the "Mapping consists of UMI reads" option.

Image annotatebarcode2
Figure 6.88: 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 Samples guide or the Identify QIAseq DNA Variants workflow, the annotations are always based on UMI reads.

Note that the counts generated by the tool may differ from the counts generated by the variant callers. First, the tool ignores reads where the forward and reverse reads do not agree. Second, the variant callers take into account quality score and frequency of sequencing errors when computing counts and they may ignore broken pairs and/or non-specific matches based on user settings. For more details see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Variant_tracks.html and https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=General_filters.html.