High Resolution Ancestry Deconvolution for High Throughput Sequencing Data

References:

• Hilmarsson H, Kumar AS, Rastogi R, Bustamante CD, Montserrat DM, Ioannidis AG. High resolution ancestry deconvolution for next generation genomic data. bioRxiv 2021 Sept 21.

• G-Nomix on GitHub

• Module Name: gnomix (see the modules page for more information)
• Multithreaded - specify number of threads in the run's config.yaml in the n_cores setting.
• Environment variables set
  • GNOMIX_HOME
• Example files in $GNOMIX_HOME/demo and $GNOMIX_HOME/demo.ipynb.
• Template configuration file's path is $GNOMIX_HOME/config.yaml
• Pretrained models in /fdb/gnomix/

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

[user@biowulf]$ sinteractive --mem 32g
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 gnomix

[user@cn3144 ~]$ cp $GNOMIX_HOME/config.yaml .
[user@cn3144 ~]$ gnomix.py $GNOMIX_HOME/demo/data/small_query_chr22.vcf.gz demo_output 22 True /fdb/gnomix/pretrained_gnomix_models/chr22/model_chm_22.pkl
...
--------------------------------------------------------------------------------
-----------------------------------  Gnomix  -----------------------------------
--------------------------------------------------------------------------------
When using this software, please cite:
Helgi Hilmarsson, Arvind S Kumar, Richa Rastogi, Carlos D Bustamante,
Daniel Mas Montserrat, Alexander G Ioannidis:
"High Resolution Ancestry Deconvolution for Next Generation Genomic Data"
https://www.biorxiv.org/content/10.1101/2021.09.19.460980v1
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Launching in pre-trained mode...
Loading model...
Launching inference...
Loading and processing query file...
- Number of SNPs from model: 317408
- Number of SNPs from file: 317408
- Number of intersecting SNPs: 317404
- Percentage of model SNPs covered by query file: 100.0%
Inferring ancestry on query data...
Phasing individual 9/9
Writing phased SNPs to disk...
Saving results...
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load gnomix
gnomix.py $GNOMIX_HOME/demo/data/small_query_chr22.vcf.gz demo_output 22 True /fdb/gnomix/pretrained_gnomix_models/chr22/model_chm_22.pkl

Submit this job using the Slurm sbatch command.

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

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

gnomix.py $GNOMIX_HOME/demo/data/small_query_chr22.vcf.gz demo_output 22 True /fdb/gnomix/pretrained_gnomix_models/chr22/model_chm_22.pkl
...
...

Submit this job using the swarm command.

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