Variant Classifier
Examples
We have included two examples. The first example, Human, uses automatically generated annotation from Ensembl. The second example, the corona virus, uses a hand-formatted annotation file. Running either example once the annotation has been prepared is identical. Sample run output is also included in the Examples directories.
Human Example
In the human directory, you will find the classify_variants /input_snps file and the in the annotation_extraction/ bcl2.coding_info file, you can find the extracted annotation file. An example of how to run classification can be found in the example.csh file. To run, cd into the Examples/human/clasify_variants directory and run:
../../../Classify_SNPs.pl \
-s input_snps \
-c ../annotation_extraction/bcl2.coding_info \
-n ../annotation_extraction/bcl2.fasta \
-o output
Corona Virus Example
In the corona_virus directory, you will find the corona_virus/example.snps file and the corona_virus/SARS-WT-annotated.coding_info file, which are the query snps and annotation file, respectively. An example of how to run the classification can be found in the example.csh file. To run, cd into the Examples/corona_virus/classify_variants directory and run:
../../Classify_SNPs.pl \
-s example.snps \
-c SARS-WT-annotated.coding_info \
-n SARS-WT-annotated.fasta \
-o example.out
For more information on the query snps, annotation and outputs, click on their respective links. If you are having trouble executing the code, please see the Frequently Asked Questions.