Description

Contains all the vcf* commands which previously lived in the htslib repository (such as vcfcheck, vcfmerge, vcfisec, etc.) and the samtools BCF calling from bcftools subdirectory of samtools

Version

• 1.2

Authorized Users

• CIRCE account holders
• RRA account holders
• SC account holders

Platforms

• CIRCE cluster
• RRA cluster
• SC cluster

Modules

BCFtools requires the following module file to run:

• apps/bcftools/1.2

• See Modules for more information.

Running BCFtools on CIRCE/SC

The BCFtools 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 BCFtools, and execute the BCFtools 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/bcftools/1.2
[user@wh-520-4-1 ~]$ bcftools query -f '%CHROM  %POS  %REF  %ALT{0}\n' file.vcf.gz

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 have wish to extract fields from VCF or BCF files and outputs them in your own format, you would set up a submit script to use bcftools like this

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

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

# Load the bcftools module:
module load apps/bcftools/1.2

# Start bcftools
bcftools query -f '%CHROM  %POS  %REF  %ALT{0}\n' file.vcf.gz

 
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 ./bcftools-test.sh

• You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

• BCFTools Home Page:
  • https://github.com/samtools/bcftools
• BCFTools Documentation:
• http://www.htslib.org/doc/bcftools.html

More Job Information

See the following for more detailed job submission information:

• SLURM User’s Guide
• Scheduling and Dispatch Policies
• Advanced Submit Techniques

Reporting Bugs

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