PAINTOR is a statistical fine-mapping method that integrates functional genomic data with association strength from potentially multiple populations (or traits) to prioritize variants for follow-up analysis. The software runs on multiple fine-mapping loci and/or populations/traits simultaneously and takes as input the following data for each set of SNPs at a locus

• Summary Association Statistics (Z-scores)
• Linkage Disequilibrium Matrix/Matrices (Pairwise Pearson correlations coefficients between each SNP)
• Functional Annotation Matrix (Binary indicator of annotation membership (i.e. if entry {i,k} = 1, then SNP i is a member of annotation K).

References:

• Integrating Functional Data to Prioritize Causal Variants in Statistical Fine-Mapping Studies. Kichaev et al, PLOS Genetics, 2014
• Leveraging Functional-Annotation Data in Trans-ethnic Fine-Mapping Studies. Kichaev and Pasaniuc, Am J Hum Genet, 2015.
• Improved methods for multi-trait fine mapping of pleiotropic risk loci. Kichaev et al, Bioinformatics, 2017.

• PAINTOR Main Site

• Module Name: PAINTOR (see the modules page for more information)
• Singlethreaded
• Example files in /usr/local/apps/PAINTOR/SampleData

Allocate an interactive session and run the program.
Sample session (user input in bold):

[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 PAINTOR

[user@cn3144 ~]$ cp -pr /usr/local/apps/PAINTOR/SampleData  /data/$USER 

[user@cn3144 ~]$ cd /data/$USER

[user@cn3144 ~]$ PAINTOR -input SampleData/input.files    -in SampleData/  \
      -out SampleData/    -Zhead Zscore -LDname ld    -enumerate 2   -annotations DHS
Running PAINTOR with full enumeration
Maximum number of causals per locus: 2
Proportion of LD variance kept when performing truncated SVD for estimating N*h2g: 0.95
Model annotations: DHS
**********
Reading in files for: Locus1
[....]
Enrichment estimates at iteration 11 is :
 4.15975
-1.88218
Average log bayes factor: 658.648

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

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

#!/bin/bash
set -e
module load PAINTOR
cp -pr /usr/local/apps/PAINTOR/SampleData  /data/$USER
PAINTOR -input SampleData/input.files    -in SampleData/  \
      -out SampleData/    -Zhead Zscore -LDname ld    -enumerate 2   -annotations DHS

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] PAINTOR.sh

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

PAINTOR -input dir1/input.files    -in dir1/  -out dir1  -Zhead Zscore -LDname ld  -enumerate 2 -annotations DHS
PAINTOR -input dir2/input.files    -in dir2/  -out dir1  -Zhead Zscore -LDname ld  -enumerate 2 -annotations DHS
PAINTOR -input dir3/input.files    -in dir3/  -out dir1  -Zhead Zscore -LDname ld  -enumerate 2 -annotations DHS

Submit this job using the swarm command.

swarm -f PAINTOR.swarm [-g #] --module PAINTOR