seismic list

Purpose

seismic list scans per-position mutation rate tables and writes a list of positions that pass specified quality criteria. Use it to identify high-quality or low-quality positions, or to create an exclusion list for seismic filter’s --mask-pos-file option.

Inputs

Table CSV files or table output directories: Per-position mutation rate tables from seismic table. See Specify Input Files.

Outputs

One list file per input table, written to {out}/{sample}/list/{ref}/{reg}/.

{step}-position-list.csv: One row per position that passed the filters. See List of Positions.

Quick example

List positions with at least 1000 informative reads:

seismic list out/sample-1/filter/ref-1

Options

Position quality thresholds

--min-ninfo-pos N: Include only positions with at least N informative reads (default 1000).
--max-fmut-pos F: Include only positions with at most fraction F mutated reads (default 1.0).

Branches

--branch NAME (-b): Write outputs to {out}/{sample}/list_{NAME}/. See Branches.

Performance

--num-cpus N — multiprocessing; see Parallelize Tasks. --force — overwrite existing outputs.

The auto-generated Command Line Reference lists every option with its current default.