Output from the Identify Variants (TAS-HD) workflow
The outputs generated are:
- Read Mapping (
) The mapped sequencing reads. The reads are shown in different colors depending on their orientation, whether they are single reads or paired reads, and whether they map unambiguously (see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Coloring_mapped_reads.html).
- Target Regions Coverage (
) The target regions coverage track shows the coverage of the targeted regions. Detailed information about coverage and read count can be found in the table format, which can be opened by pressing the table icon found in the lower left corner of the View Area.
- Target Regions Coverage Report (
) The report consists of a number of tables and graphs that in different ways provide information about the targeted regions.
- Identified Variants and Indels Indirect Evidence (
) A variant track containing the variants identified by the Fixed Ploidy Variant Detection tool, and a variant track with the indels inferred from indirect evidence by the Structural Variant Caller. The variants can be shown in track format or in table format. When holding the mouse over the detected variants in the Track List, a tooltip appears with information about the individual variants. You will have to zoom in on the variants to be able to see the detailed tooltip.
- Genome Browser View Identify Variants (
) A collection of tracks presented together. Shows the annotated variant track together with the human reference sequence, genes, transcripts, coding regions, the mapped reads, the identified variants, and the structural variants (see figure 20.32).