LASER

Description

From the LASER Home Page: LASER is a program to estimate individual ancestry by directly analyzing shotgun sequence reads without calling genotypes. LASER uses principal components analysis (PCA) and Procrustes analysis to analyze sequence reads of each sample and place the sample into a reference PCA space constructed using genotypes of a set of reference individuals. With an appropriate reference panel, the estimated coordinates of the sequence samples reflect their ancestral background and can be used to correct for population stratification in association studies. LASER can accurately estimate ancestry even with modest amounts of data, such as the off-target sequence data generated by targeted sequencing experiments.

In version 2.0 or later, the software package includes a new program TRACE for tracing an individual’s genetic ancestry based on genotype data. TRACE follows the same analysis framework as LASER and can accurately place study samples into a reference ancestry space using a relatively small number of genotypes. When using the same reference panel, LASER and TRACE can place sequenced and genotyped samples into the same ancestry space.

LASER can also perform standard PCA on genotype data to explore population structure and to create the reference ancestry space. Different options to compute PC scores and PC loadings have been implemented in the LASER program (version 2.01 or later).

Version

  • 2.02

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

LASER requires the following module file to run:

  • apps/laser/2.02

Running LASER on CIRCE/SC

The LASER user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Interactive Mode

Next, use the following commands to open an SRUN Interactive Session, load the module for LASER, and execute the LASER binary:

[user@login0 ~]$ srun --time=48:00:00 --nodes=1 --ntasks-per-node=1 --pty /bin/bash
[user@wh-520-4-1 ~]$ module load apps/laser/2.02
[user@wh-520-4-1 ~]$ laser -s pileup2seq/test.seq  -g resource/HGDP/HGDP_938.geno \
-c resource/HGDP/HGDP_938.RefPC.coord -o test -k 2

Batch Job submission

To run batch jobs on the CIRCE/SC cluster, users will need to submit their jobs to the scheduling environment if their jobs take more than 20 minutes to run on a standard PC.

If, for example, you wish to estimate ancestries of sequence samples, you would set up a submit script to use laser like this

#!/bin/bash
#
#SBATCH --job-name=laser-test
#SBATCH --time=01:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --output=output.%j.laser-test

#### SLURM 1 processor LASER test to run for 1 hours.

# Load the laser module:
module load apps/laser/2.02

# Start LASER
laser -s pileup2seq/test.seq  -g resource/HGDP/HGDP_938.geno \
-c resource/HGDP/HGDP_938.RefPC.coord -o test -k 2

 
Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./laser-test.sh
  • You can view the status of your job with the “squeue -u <username>” command

Documentation

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

  • LASER Examples:
    • /apps/laser/2.02/example - includes genotype data from the Human Genome Diversity Panel
    • /apps/laser/2.02/pileup2seq - command line examples for use of pileup2seq.py (make sure to add module for Python before using)
    • /apps/laser/2.02/plot - example R code to generte figures (make sure to add module for R before using)
    • /apps/laser/2.02/vcf2geno - command line example for use of vcf2geno

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with LASER to the IT Help Desk: rc-help@usf.edu