SIFT missense predictions for genomes

SIFT (sorting intolerant from tolerant) predicts whether an amino acid substitution is deleterious. It is used in disease, mutation and genetic studies. Users can get predictions for single-nucleotide variants from their organism of interest using the SIFT 4G annotator with SIFT 4G's precomputed databases. 1. Download the desired databaseThis dataset provides SIFT predictions for ~50 genomes. Format is <species_name>_<genome_build>.zip Extract the downloaded zip file.unzip <species_name>_<genome_build>.zip The unzipped folder will have three files for each chromosome: a compressed chromosome file (.gz) a regions file (.regions) a chromosome statistics file (.txt) 2. Download SIFT 4G Annotator: SIFT4G_Annotator.jarThis is a java executable (.jar)3. Annotate variants in a VCF file java -jar <Path to SIFT4G_Annotator> -c -i <Path to input vcf file> -d <Path to SIFT4G database directory> -r <Path to your results folder> -t Note: To run the Annotator via command line "-c" is essential (see the commandline parameters in the table below). If "-t" option is not used SIFT 4G extracts annotator single transcript per variant. The VCF file must have 8 columns, including the INFO column because SIFT annotations will be added there. Command line Options: Option Description -c To run on command line -i Path to your input variants file in VCF format -d Path to SIFT database directory -r Path to your output results folder -t To extract annotations for multiple transcripts (Optional) Code used to build these databases:- https://github.com/pauline-ng/SIFT4G_Create_Genomic_DB- https://github.com/rvaser/sift4g