skip to main content
Roche logo
4. GS De Novo Assembler and GS Reference Mapper Appendices : 4.17 Target Regions and Extended Target Regions
4.17
Target Regions and Extended Target Regions
For targeted resequencing mapping projects, target regions are defined as part of the experimental design. In the GS Reference Mapper, these targeted regions are specified via the Input files section, on the Input sub-tab of the Parameters tab (Section 2.7.1).
Many targeted resequencing protocols will produce reads that extend beyond the actual target region. The sequence information from the areas just outside the target region boundaries is often useful, e.g. the intronic regions flanking exons in an exome experiment. The GS Reference Mapper reports these sequences as belonging to “extended target regions”.
Specifically, target regions and extended target regions are defined as follows (Figure 102):
•
Target regions: defined in an input file provided to the project via the Input sub-tab of the Parameters tab (or on the command line, using the –reg option). All reads and contigs that overlap a target region, and sequencing variants therein, are labeled “InRegion”.
•
Extended target regions: sum of the targeted regions and all contigs that overlap the targeted regions. The reads within these contigs that DO NOT overlap a target region, and sequencing variants therein, are labeled “InExtRegion”.
•
Any read that does not overlap with an extended target region, and any sequencing variant therein, is labeled “OutOfRegion”.
This principle applies whenever target regions are specified on the Input sub-tab, whether the DNA sample has been physically selected as part of the library preparation procedure.
Figure 102: Target regions, extended target regions, and out of target regions