NGS-Pipeline Command Line

The ngs-pipeline command line is invoked using ngs-pl executable, i.e.:

ngs-pl CMD [ARGS]

For example, to see the available commands, execute:

$ ngs-pl showcmds

The available CMDs are listed in List of Commands.

Below are an excerpt of commands that are most commonly used.

Preparation commands

cmds/generate-links`

This command generate symbolic links from a batch of files. The link names can be stripped by number of underscore (from beginning or end of filename) or by prefix. Paired-end reads will be linked properly.

prepare-sample-directory

Given a manifest file containing the sample codes and corresponding fastq files, the command will prepare the directory structure for further processing.

The basic command is:

ngs-pl prepare-sample-directory -o OUTDIR -i MANIFEST_FILE INPUTDIR

OUTDIR is the target directory where sample directories will be created. INPUTDIR is the source directory where the read files to be prepared are reside. MANIFEST_FILE is a tab-delimited file with header of SAMPLE and FASTQ, for the sample codes and their corresponding FASTQ files, respectively.

[TODO: provide example manifest file]

Execution commands

run-sample-variant-caller

Run the individual sample variant calling pipeline in parallel, which will go through mapping reads, processing mapped reads, and performing all necessary process up to getting GVCF files

run-joint-variant-caller

Run the joint variant calling pipeline to process GVCF files into multi-sample VCF files. This command can be run after completing run-sample-variant-caller

ngs-pl run-targeted-variant-caller

Run targeted variant calling pipeline to produce single-sample VCF file for each sample. Multi-sample VCF file then can be generated by using bcftools merge.

run-multistep-variant-caller

Run the multistep variant caller from single command, basically by executing generate-manifest, prepare-sample-directory, run-sample-variant-caller and run-joint-variant-caller consecutively.