Option | Description |
|---|---|
Pile-up pane | |
Open a tooltip with the following information for a specific read (variant or non-variant): • Read name • Read direction • Read CIGAR string • Read Tags | SHIFT + click the mouse scroll wheel, or CTRL +SHIFT, and then left mouse click. |
Open a tooltip with the following information for a specific variant: • The position number for the allele • The major allele at the position • The read direction for the allele • The counts for the different alleles at the position • The total coverage for the position • The Allele Balance Ratio • The Allele Balance Score | Click the mouse scroll wheel or CTRL + left mouse click. |
Add variant at position <n> | |
Jump to position | Note: Jump to position moves the Pile-up pane left or right—you are moving the display to a particular variant position.The Reference position, therefore, changes accordingly in the Reference pane. Right-click any position, and on the context menu that opens, click Jump to Position. In the Position Input dialog box that opens, enter the position number to move the viewer to. The position is displayed in the middle of the viewer. |
Jump to line | Note: Jump to line moves the Pile-up pane up and down—you are moving the display to a particular read.The Reference position, therefore, does not change in Reference pane. Right-click any position, and on the context menu that opens, click Jump to line. In the Position Input dialog box that opens, enter the line number to move the viewer to. The read is displayed as the top of the Pile-up pane. |
Go to closest position in table | Right-click any position, and on the context menu that opens, select this option to highlight the entry in the Variants table for the variant that is closest to this selected position. |
Copy Read’s Sequence | To copy the sequence from any read to your clipboard, right-click any read, and on the context menu that opens, click Copy Read’s Sequence. You can then use standard Paste commands to paste the copied information into a third-party product such as Microsoft Word or Notepad. |
Remove Read/Undo Remove Read | Right-click any position, and on the context menu that opens, select this option to remove the read from any consideration when analyzing or graphing the project results. A solid horizontal black line is displayed across the read to indicate that it has been removed. To add a removed read back, right-click the read, and on the context menu that opens, click Undo Remove Read. Note: If the removed read contains any called variants, then these variants are highlighted in light blue in the Variants table. See Variants table. |
Variants table | |
Copy selected | Click and hold the left mouse button and then draw a box (square or rectangle) around the cells that are being copied. Right-click any of the copied cells, and on the context menu that opens, select Copy selected to copy the selected table cells to your clipboard. Use standard keyboard commands or menu commands to paste the copied cells into a third-party application such as Microsoft Word or Excel. |
Deleting a variant | |
Saving/Loading reports | |