SVPV Plot Windows
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Continuous windows display a single region. Read depth, insert mapping distance and alignments stats are shown at the same scale.
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Zoom windows also display a single region, however only the depth track is presented for the entire region. Insert mapping distance and alignment stats are shown in Zoomed windows around the breakpoints.
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Split windows display two regions side by side, the same as Continuous.
- The default window length is 3 times the length of the SV. This is controlled by the parameter exp (with default value of 1 meaning 1 times SV length added to either side). The read depth will be shown for the entirety of this window in all cases.
- If the length of this window is larger than bkpt_win x rd_len, then the SV will be plotted with a Zoom window rather than a Continuous window.
- Zoom windows show the insert mapping distance and alignments stats centred at the breakpoints with window size defined by bkpt_win x rd_len.
- The smallest Continuous window size that will be presented is equal to bkpt_win x rd_len.
Insertions are presented using a Continuous window of size bkpt_win x rd_len.
Translocations are presented using a Split window, with each window of size bkpt_win x rd_len.
| Parameter | Default | Description |
|---|---|---|
| rd_len | 100 | The read length of the sequencing platform |
| exp | 1 | Expansion around SVs to define the plot window |
| bkpt_win | 5 | Number of read lengths to set windows around breakpoints |