process_nps¶
The gamtools process_nps tool is used to map raw sequencing data
from a collection of NPs and call positive windows from those NPs
to generate a segregation table. It can optionally also calculate
various QC metrics for each NP, generate bigwig/bed files for
visualising the raw data and calculate proximity matrices.
Usage and option summary¶
Usage:
gamtools process_nps [OPTIONS] -g <GENOME_FILE> <FASTQ_FILE> [<FASTQ_FILE> ...]
Optional parameters:
| Option | Description |
|---|---|
| -o, –output_dir | Write segregation, matrix etc. to this directory |
| -q, –minimum-mapq | Filter out any mapped read with a mapping quality less than x (default is 20, use -q 0 for no filtering) |
| -c, –do-qc | Perform sample quality control. |
| -i, –bigwigs | Make bigWig files. |
| -b, –bigbeds | Make bed files of positive windows |
| -w, –window-sizes | One or more window sizes for calling positive windows |
| -s, –matrix-sizes | Resolutions for which proximity matrices should be produced. |
| –qc-window-size | Use this window size for qc (default is median window size). |
| -f, –fittings_dir | Write segregation curve fitting plots to this directory |
| -d, –details-file | If specified, write a table of fitting parameters to this path |
| –additional-qc-files | Any additional qc files to filter on |
Parameters inherited from doit:
gamtools process_nps uses doit as a task dependency engine, to
determine what actions need to be performed and in which order. A number
of additional command line parameters are available that control doit’s behaviour.
| Option | Description |
|---|---|
| –doit-db-file | Doit saves information about each run in a database file. This parameter specifies the location of that database file. |
| –doit-backend | Doit database format. (one of sqlite3, json, dbm. default: dbm) |
| –doit-verbosity | 0 capture (do not print) stdout/stderr from task.
1 capture stdout only.
2 do not capture anything (print everything
immediately). Default: 1 |
| –doit-reporter | Where should doit report the output from each task. One of (json, console, zero, executed-only). Default: console |
| –doit-process | Number of subprocesses (default is 0, i.e. serial processing) |
| –doit-parallel-type | Tasks can be executed in parallel in different ways:
process: uses python multiprocessing module
thread: uses threads. Default is process. |