annotated_snps_filter.R is an
R script cross-references annotated SNP files created using annotating_snps.R. It takes two files created using this script, and returns unique SNPs for each file. If a SNP in File 1 is not found at the same position on the same sequence as File 2, it is returned as a unique SNP, and vice versa. These unique SNPs are then written to new
To use this script, variables need to be defined on lines 21 and 22 of the script:
- Assign the name of the first annotated SNP file to be filtered to ‘annotated_SNP_file_1’.
- Assign the name of the second annotated SNP file to be filtered to ‘annotated_SNP_file_2’.
- These files should be in the
- Optional: the name of the output files can be assigned on lines 109 and 115 respectively.