GenoTools is a suite of automated genotype data processing steps written in Python. The core pipeline was built for Quality Control and Ancestry estimation of data in the Global Parkinson's Genetics Program (GP2).

References:

• Dan Vitale, Mathew J Koretsky, Nicole Kuznetsov, Samantha Hong, Jessica Martin, Mikayla James, Mary B Makarious, Hampton Leonard, Hirotaka Iwaki, Faraz Faghri, Cornelis Blauwendraat, Andrew B Singleton, Yeajin Song, Kristin Levine, Ashwin Ashok Kumar Sreelatha, Zih-Hua Fang, Mike Nalls. GenoTools: An Open-Source Python Package for Efficient Genotype Data Quality Control and Analysis. G3 Genes|Genomes|Genetics, 2024; jkae268

• GenoTools on GitHub

• Module Name: genotools (see the modules page for more information)
• Reference data (from genotools-download) in /fdb/genotools/

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 genotools

[user@cn3144 ~]$ genotools --help

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

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

#!/bin/bash
set -e
module load genotools

genotools \
  --pfile /path/to/genotypes/for/qc \
  --out /path/to/qc/output \
  --ancestry \
  --ref_panel /fdb/genotools/ref_panel/1kg_30x_hgdp_ashk_ref_panel \
  --ref_labels /fdb/genotools/ref_panel/1kg_30x_hgdp_ashk_ref_panel_labels.txt \
  --all_sample \
  --all_variant

Submit this job using the Slurm sbatch command.

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

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

genotools --pfile sample1/genotypes --out sample1/qc --ancestry --ref_panel /fdb/genotools/ref_panel/1kg_30x_hgdp_ashk_ref_panel --ref_labels /fdb/genotools/ref_panel/1kg_30x_hgdp_ashk_ref_panel_labels.txt --all_sample --all_variant
genotools --pfile sample2/genotypes --out sample2/qc --ancestry --ref_panel /fdb/genotools/ref_panel/1kg_30x_hgdp_ashk_ref_panel --ref_labels /fdb/genotools/ref_panel/1kg_30x_hgdp_ashk_ref_panel_labels.txt --all_sample --all_variant
genotools --pfile sample3/genotypes --out sample3/qc --ancestry --ref_panel /fdb/genotools/ref_panel/1kg_30x_hgdp_ashk_ref_panel --ref_labels /fdb/genotools/ref_panel/1kg_30x_hgdp_ashk_ref_panel_labels.txt --all_sample --all_variant

Submit this job using the swarm command.

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