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gwas-gene-discovery

The script map_snp_to_genes.py searches through tabular GWAS results from the GAPIT outputs and returns user with suspected causative genes for ESV in the rice samples subject to investigation.

Parameters

The script needs the following inputs to work:

  • A tabular file of GWAS results containing id, position, chromosome number, p-value of SNPs etc in csv.
  • A user defined logP threshold (-log10p-value)
  • A genomic reference provided from International Rice Research Institute in txt.

Please run the script as the following for more help on parameters and usage

python map_snp_to_gene_v5.py -h

Demonstration

The following command

python map_snp_to_gene_v5.py -f GAPIT.MLM.DTF.GWAS.Results.csv -p 7

Produced the folder /GAPIT.MLM.DTF.GWAS.Results By changing the -f parameter to GAPIT.MLM.blupWidth.GWAS.Results.csv created the folder GAPIT.MLM.blupWidth.GWAS.Results The user may wish to delete one or both of the folders to replicate this step.