This chapter describes only import/export functionality specific to the Biomedical Genomics Analysis.
Data import is generally done using the standard tools of the CLC Genomics Workbench. This includes the on-the-fly import functionality available when launching workflows, described at:
Direct access to certain NGS importers is also provided via the Analyze QIAseq Panels tool, as described in this section.
Reference data import is described in Reference Data Management.
VCF (Biomedical) exporter
The Biomedical Genomics Analysis plugin provides a VCF exporter that extends the functionality of the standard VCF exporter by supporting the export of CNV tracks and fusion tracks, in addition to the export of variant tracks.
The standard VCF exporter is described at https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Export_in_VCF_format.html.
Compared with the standard exporter, an additional option is present in the export dialog to export multiple inputs as a single file (figure 2.1). When this option is selected, a CNV track, fusion track and variant track can be exported together into a single VCF file. Note however that when this is selected, only a single variant track can be exported at a time unless the exporter is run in "batch" mode.
VCF format files can be uploaded directly to QCI Interpret, or the Upload to QCII tool can be used to upload data from CLC Genomics Workbench without explicitly exporting it first. Use of Upload to QCII is described in QCI Interpret Integration.
SAM/BAM export of UMI read mappings When exporting UMI reads to SAM or BAM format, a UMI will be described as Unique_Molecular_Index=[number1]_count=[number2]. Here number1 is a UMI ID (just a unique UMI group number), and number2 is the number of reads that are in that UMI group.
This information is relevant to the export of relevant outputs from workflows distributed with this plugin for analyzing data generated using some types of QIAseq panels, such as:
- Targeted DNA Panels
- Targeted RNAscan Panels
- UPX 3' RNA Panels
- Multimodal Panels
- RNA Fusion XP