CAVIAR (CAusal Variants Identication in Associated Regions), is a statistical framework that quantifies the probability of each variant to be causal while allowing with arbitrary number of causal variants.

References:

• Farhad Hormozdiari, Ayellet V. Segre, Martijn van de Bunt, Xiao Li, Jong Wha J Joo, Michael Bilow, Jae Hoon Sul, Bogdan Pasaniuc and Eleazar Eski. Joint Fine Mapping of GWAS and eQTL Detects Target Gene and Relevant Tissue. The American Journal of Human Genetics (AJHG). doi:10.1016/j.ajhg.2016.10.003
• Farhad Hormozdiari, Emrah Kostem, Eun Yong Kang, Bogdan Pasaniuc and Eleazar Eskin. Identifying Causal Variants at Loci with Multiple Signals of Association. Genetics, 44, 725–731 (2014). doi:10.1534/genetics.114.167908

• CAVIAR Main Site

• Module Name: caviar (see the modules page for more information)
• Multithreaded/singlethreaded/MPI...
• environment variables set
  • CAVIAR_HOME
• Example files in $CAVIAR_HOME/sample_data

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

[user@biowulf]$ sinteractive --gres lscratch:1
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 caviar
[+] Loading caviar, version a97e614...
[user@cn3144 ~]$ cd /lscratch/$SLURM_JOBID
[user@cn3144 46116226]$ cp -r $CAVIAR_HOME/sample_data/* .
[user@cn3144 46116226]$ CAVIAR -l DDB1.top100.sig.SNPs.ld -z DDB1.top100.sig.SNPs.ZScores -o outfile
@-------------------------------------------------------------@
| CAVIAR!|    v2.0         |  01/Aug/2017 | 
|-------------------------------------------------------------|
| (C) 2017 Farhad Hormozdiari, GNU General Public License, v2 |
|-------------------------------------------------------------|
| For documentation, citation & bug-report instructions:      |
| http://genetics.cs.ucla.edu/caviar/            |
@-------------------------------------------------------------@
00
add
1.73212e-750.1
FINISH
reach=100
100
Max Causal=2
Total=5051
0 1.36408e-06
Total Likelihood= 4.552733e+48 SNP=100 

56 5.000000e-01
53 9.999984e-01

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

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

#!/bin/sh

set -e

module load caviar
cp -r $CAVIAR_HOME/sample_data/* .
CAVIAR -l DDB1.top100.sig.SNPs.ld -z DDB1.top100.sig.SNPs.ZScores -o outfile

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] caviar.sh

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

CAVIAR -l ldfile1 -z zfile1 -o outfile1
CAVIAR -l ldfile2 -z zfile2 -o outfile2
CAVIAR -l ldfile3 -z zfile3 -o outfile3
CAVIAR -l ldfile4 -z zfile4 -o outfile4

Submit this job using the swarm command.

swarm -f caviar.swarm [-g #] [-t #] --module caviar