p3-submit-variation-analysis

Submit a Variation Analysis Job

This script submits a Variation Analysis job to BV-BRC. It takes input from read libraries and looks for small differences against a reference genome.

Usage Synopsis

p3-submit-variation-analysis [options] output-path output-name

Start a variation analysis, producing output in the specified workspace path, using the specified name for the base filename of the output files.

Command-Line Options

The following options are used to assist in the specification of files. Files specified in the options that are in the workspace should have a ````ws:> prefix. All others are assumed to be local.

  • –workspace-path-prefix

Base workspace directory for relative workspace paths.

  • –workspace-upload-path

Name of workspace directory to which local files should be uplaoded.

  • –overwrite

If a file to be uploaded already exists and this parameter is specified, it will be overwritten; otherwise, the script will error out.

The following options specify the reads to be analyzed.

  • –paired-end-lib

Two paired-end libraries containing reads. These are coded with a single invocation, e.g. --paired-end-lib left.fa right.fa. The libraries must be paired FASTQ files. A prefix of ws: indicates a file is in the BV-BRC workspace; otherwise they are uploaded from the local file system. This parameter may be specified multiple times.

  • –single-end-lib

A library of single reads. This must be a FASTQ file. A prefix of ws: indicates a file is in the BV-BRC workspace; otherwise they are uploaded from the local file system. This parameter may be specified multiple times.

  • –srr-id

A run ID from the NCBI sequence read archive. The run will be downloaded from the NCBI for processing. This parameter may be specified multiple times.

The following options modify the analysis process.

  • –reference-genome-id

The ID of the genome in BV-BRC to be used as a reference.

  • –mapper

Mapping utility to use– BWA-mem, BWA-mem-strict, Bowtie2, or LAST. Default is BWA-mem.

  • –caller

SNP-calling utility to use– FreeBayes or SAMtools. Default is FreeBayes.

These options are provided for user assistance and debugging.

  • –help

Display the command-line usage and exit.

  • –dry-run

Display the JSON submission string and exit without invoking the service or uploading files.