gratools depth_nodes_stat

Options

Usage Examples

Display statistics about the node depth

This command analyzes how many samples share each segment (node) in the graph and presents a summary table.

$ gratools depth_nodes_stat --gfa Og_cactus.gfa.gz --filter-len 50 --threads 4

────────────────  Summary ────────────────────────────────────────
Total segments analyzed: 2,354,995
Total segments passing length filter: 210,046 (8.92%)

          Node Depth Statistics — Og_cactus (Len ≥ 50bp)
╭───────┬──────────┬────────────┬───────────────────┬────────────╮
│ Depth │ Segments │ Percentage │ Filtered Segments │ Filtered % │
├───────┼──────────┼────────────┼───────────────────┼────────────┤
│   1   │ 575,292  │   24.43%   │       1,257       │   0.60%    │
│   2   │ 316,053  │   13.42%   │       7,345       │   3.50%    │
│   3   │ 301,588  │   12.81%   │       5,604       │   2.67%    │
│   4   │ 501,321  │   21.29%   │      11,500       │   5.47%    │
│   5   │ 660,741  │   28.06%   │      184,340      │   87.76%   │
╰───────┴──────────┴────────────┴───────────────────┴────────────╯

Columns Explanation

  1. Depth: The number of unique samples that a segment is found in. For example, a depth of 1 means the segment is private to a single sample.

  2. Segments: The total count of segments at that specific depth.

  3. Percentage: The proportion of segments at this depth relative to the total number of segments in the GFA.

  4. Filtered Segments: The count of segments at this depth that are longer than the size specified by the --filter-len option.

  5. Filtered %: The proportion of filtered segments at this depth relative to the total number of filtered segments (shown in the summary header).

Filter Option

The --filter-len (or -fl) option takes an integer value. This value is used to populate the Filtered Segments and Filtered % columns. In the example above, a filter of 50 was used, meaning these columns only account for segments that are 50 base pairs or longer.