Quick Links Interactive job Batch job on Biowulf Parallel job on Biowulf Swarm of jobs

vcflib is a C++ library for parsing Variant Call Format (VCF) files and a set of command line tools based on that library.

The following tools are currently available:

There may be multiple versions of vcflib available. An easy way of selecting the version is to use modules. To see the modules available, type

module avail vcflib 

To select a module use

module load vcflib/[version]

where [version] is the version of choice.

Environment variables set

• $PATH
• $CPATH

Web sites

• GitHub

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ vcf=/fdb/GATK_resource_bundle/hg19-2.8/CEUTrio.HiSeq.WGS.b37.bestPractices.hg19.vcf.gz

[user@cn3144 ~]$ vcfsamplenames $vcf
NA12878
NA12891
NA12892

[user@cn3144 ~]$ zcat $vcf | vcfcountalleles
12935193

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch script similar to the following example:

#! /bin/bash

function fail() {
    echo "$@" >&2
    exit 1
}

rb=/fdb/GATK_resource_bundle/hg19-2.8
module load vcflib || fail "could not load vcflib module"
module load samtools/1.2 || fail "could not load samtools module"
tabix -h ${rb}/CEUTrio.HiSeq.WGS.b37.bestPractices.hg19.vcf.gz chr1:1-100000 \
 | vcf2tsv > CEUTrio.out

b2$ sbatch vcf2tsv.sh

Create a swarm command file similar to the following example:

vcfannotate -b enhancers.bed -k enh sample1.vcf > sample1_anno.vcf
vcfannotate -b enhancers.bed -k enh sample2.vcf > sample2_anno.vcf

And submit to the queue with swarm

b2$ swarm -f vcfannotate.swarm -g 5