This Bash script is designed for processing a VCF file and generating a Polygenic Risk Score (PRS) for each individual in the file. It filters VCF files based on a provided GWAS table, converts the filtered VCF to PLINK format, and calculates PRS using PLINK.
- bcftools
- htslib
- PLINK1.9 and PLINK2
- SLURM Workload Manager (for job memory and CPU allocation)
Ensure that all required software (bcftools, htslib, PLINK1.9, PLINK2) is installed on your system. If you're using a cluster environment, these might already be available as modules. Also, change hard coded paths to PLINK executables to your correct path. If you are using a different GWAS table, you may need to change the numbers for the score PLINK function to select the correct columns in this order:
- variant id
- effect allele
- effect size
To run the script, provide it with two arguments: the input VCF file (compressed with .gz) and the GWAS table in text format. The VCF should be indexed as well.
./gwas_vcf_processor.sh <input_vcf>.vcf.gz <gwas_table>.txt- <input_vcf>.vcf.gz - The input VCF file (compressed)
- <gwas_table>.txt - The GWAS table
The script will output a tsv file containing two columns: id and prs. The file is a list of the calculated PRS for each individual in the VCF file.
- Bellenguez, C., Küçükali, F., Jansen, I.E., et al. (2022). New insights into the genetic etiology of Alzheimer’s disease and related dementias. Nature Genetics, 54, 412-436. https://doi.org/10.1038/s41588-022-01024-z
- Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li. "Twelve years of SAMtools and BCFtools." GigaScience, Volume 10, Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008
For support or contributions, please contact me at:
jtaylor[at]hudsonalpha.org