Annotated SNPs filter

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 .tsv files.

Usage

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 ~/bioinfo-notebook/data/ directory.
• Optional: the name of the output files can be assigned on lines 109 and 115 respectively.

See also

• annotated_snps_filter.R on GitHub
• annotating_snps.R
• File formats used in bioinformatics
• snp_calling.sh, a script for generating VCF files of SNPs.
• genome_annotation_SwissProt_CDS.sh, a script for generating genome annotation GFF files.