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Vcflib on Biowulf

Vcflib is a simple C++ library for parsing and manipulating VCF files, + many command-line utilities


Running an interactive job

Users may need to run jobs interactively sometimes. Such jobs should not be run on the Biowulf login node. Instead allocate an interactive node as described below, and run the interactive job there.


biowulf $ qsub -I -l nodes=1:g24:c24
qsub: waiting for job 2236960.biobos to start
qsub: job 2236960.biobos ready

[user@pXXX]$ module load vcflib
        
[user@pXXX]$ cd /data/$USER/XXXX

[user@pXXX]$ vcfannotategenotypes <annotation-tag> <vcf file> <vcf file>
[user@pXXX]$ exit
qsub: job 2236960.biobos completed
user@biowulf]$ 

Submitting a single delly batch job

1. Create a script file along with the lines below. Modify the path of location before running.

2.

#!/bin/bash
# This file is runVcflib
#
#PBS -N vcflib
#PBS -m be
#PBS -k oe
module load vcflib
cd /data/$USER//run1
vcfannotategenotypes <annotation-tag> <vcf file> <vcf file>

3. Submit the script using the 'qsub' command on Biowulf

$ qsub -l nodes=1:g8 /data/$USER/runVcflib

 

Submitting a swarm of delly jobs

Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.

Set up a swarm command file (eg /data/$USER/cmdfile). Here is a sample file:

cd /data/$USER/run1; vcfannotategenotypes <annotation-tag> <vcf file> <vcf file>
cd /data/$USER/run2; vcfannotategenotypes <annotation-tag> <vcf file> <vcf file>
........ ........ cd /data/$USER/run20; vcfannotategenotypes <annotation-tag> <vcf file> <vcf file>

The '-f' and '--module' options for swarm are required

By default, each line of the command file above will be executed on 1 processor core of a node and use 1gb of memory. If this is not what you want, you will need to specify '-t' and '-g' flags when you submit the job on biowulf.

Say if each line of the commands above also will need to use 10gb of memory instead of the default 1gb of memory, make sure swarm understands this by including '-g 10' flag:

biowulf> $ swarm -g 10 -f cmdfile --module vcflib

For more information regarding running swarm, see swarm.html

Documentation

https://github.com/ekg/vcflib#vcflib