Biowulf High Performance Computing at the NIH
Nirvana on Biowulf

Nirvana provides clinical-grade annotation of genomic variants (SNVs, MNVs, insertions, deletions, indels, and SVs (including CNVs). It can be run as a stand-alone package or integrated into larger software tools that require variant annotation.

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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 ~]$ module load nirvana
[+] Loading nirvana  2.0.4  on cn3144 
[+] Loading singularity  2.4.2  on cn3144 

[user@cn3144 ~]$ cp /usr/local/apps/nirvana/TEST_DATA/HiSeq.10000.vcf .

[user@cn3144 ~]$ nirvana -c /fdb/nirvana/Cache/26/GRCh37/Ensembl \
		--sd /fdb/nirvana/SupplementaryDatabase/GRCh37 \
		-r /fdb/nirvana/References/5/Homo_sapiens.GRCh37.Nirvana.dat \
		-i HiSeq.10000.vcf \
		-o Hiseq_result_anno
---------------------------------------------------------------------------
Nirvana                                             (c) 2018 Illumina, Inc.
Stromberg, Roy, Lajugie, Jiang, Li, and Kang               2.0.4-0-g511995f
---------------------------------------------------------------------------

Reference                                              Time      Variants/s
---------------------------------------------------------------------------
chr1                                                00:00:03.2        3,096

Time: 00:00:14.5

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

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. nirvana.sh). For example:

#!/bin/bash
set -e
module load nirvana
nirvana -c /fdb/nirvana/Cache/26/GRCh37/Ensembl \
		--sd /fdb/nirvana/SupplementaryDatabase/GRCh37 \
		-r /fdb/nirvana/References/5/Homo_sapiens.GRCh37.Nirvana.dat \
		-i HiSeq.10000.vcf \
		-o Hiseq_result_anno

Submit this job using the Slurm sbatch command.

sbatch nirvana.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. nirvana.swarm). For example:

nirvana -i vfc1.vcf -o vcf1 [... rest of the options]
nirvana -i vfc2.vcf -o vcf2 [... rest of the options]
nirvana -i vfc3.vcf -o vcf3 [... rest of the options]
nirvana -i vfc4.vcf -o vcf4 [... rest of the options]

Submit this job using the swarm command.

swarm -f nirvana.swarm --module nirvana
where
--module nirvana Loads the nirvana module for each subjob in the swarm