DENTIST (Detecting Errors iN analyses of summary staTISTics) is a quality control (QC) tool for summary-level data from genome-wide association studies (GWASs). It leverages the difference between the observed GWAS test-statistic of a variant and its predicted value (using the neighbouring variants and linkage equilibrium (LD) data from a reference panel) to remove problematic variants. It can detect genotyping/imputation errors in either the original GWAS or the LD reference samples, allelic errors (i.e., the effect alleles of the variants are mislabelled) in the GWAS summary data, as well as heterogeneity between the GWAS and LD reference samples.

• Chen, W., Wu, Y., Zheng, Z. et al. Improved analyses of GWAS summary statistics by reducing data heterogeneity and errors. Nat Commun 12, 7117 (2021).

• https://github.com/Yves-CHEN/DENTIST

• Module Name: dentist (see the modules page for more information)
• DENTIST can be run in a multi-threaded mode by using the --thread-num <<>num<>>
option. Only do this if you have allocated multiple processors in your sinteractive call or your job script.

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 dentist
[user@cn3144 ~]$ cd /data/$USER/dir
[user@cn3144 dir]$ dentist
*******************************************************************
* DENTIST (Detecting Errors iN analyses of summary staTISTics)
* Version 1.1.0.0
* (C) 2018 Wenhan Chen, Zhihong Zhu and Jian Yang
* The University of Queensland
* MIT License
*******************************************************************
Flags include:
--gwas-summary,--bfile,--bld,--out,
--chrID,--thread-num,--dup-threshold,--p-value-threshold,
--GWAS-pvalue-threshold,--delta-MAF,--maf,--extract,
--target,--target-bp,--radius,--with-NA-geno,
--wind-dist,--wind,--debug,--load-LD,
--iteration-num,--LD-unit-in-byte,--SVD-trunc-prop,--check-LD,
--write-LD,--freq,--impute,
[user@cn3144 dir]$ dentist --gwas-summary summary_data --bfile ref --out prefix

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

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

#!/bin/bash
set -e
module load dentist 
dentist --gwas-summary summary_data --bfile ref --out prefix

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] batch.sh

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

cd dir1; dentist --gwas-summary summary_data --bfile ref --out prefix
cd dir2; dentist --gwas-summary summary_data --bfile ref --out prefix
cd dir3; dentist --gwas-summary summary_data --bfile ref --out prefix

Submit this job using the swarm command.

swarm -f job.swarm [-g #] --module dentist