A parser for selecting a shortlist of variants from an Alamut file. By specifying a list of candidate genes generated from HPO / Phenomizer, the Alamut input is parsed and a standard ruleset applied in order to reduce the number of variants to a shortlist of potential pathogenic ones. The Alamut input is generated from an WES VCF file.
Created by Garan Jones g.jones@exeter.ac.uk
Clone the repository to a suitable directory, initiallizing Git if required;
git init
git clone https://github.com/pasted/variant_parser.git
bundle install
Help list of commands
ruby variant_parser.rb --help
General use, with output to an Excel file
ruby variant_parser.rb -v <example_alamut_file.txt> -g <example_gene_list.txt> -p <sample_id> -e
Options:
-v, --variants=<s> Filepath to Alamut file to parse.
-f, --fake-exome-depth=<s> Filepath to fake Exome Depth file to parse.
-g, --genes=<s> Filepath to text file with list of valid HGVS gene symbols - one symbol per line.
-o, --ontology-genes=<s> Filepath to CSV export from HPO web browser.
-a, --approved-genes Check gene symbols against HGNC - only process those which are the current symbol
-e, --excel-output Export results to an Excel spreadsheet.
-p, --proband-sample=<s> Proband sample ID to include in output
-c, --clinvar Include ClinVar pathogenic candidates (CliniVarClinSignifs: Pathogenic; ClinVarReviewStatus: 3 or 4; ClinVarOrigins: Germline).
-r, --research Select variants on research criteria.
-m, --maf-cutoff=<f> Set a Minor Allele Frequency (MAF) cutoff - integer out of 1 based on ExAC all populations frequencies. (Default: 0.05)
-s, --result-prefix Set the prefix for the result file output, for example Family ID. Defaults to the directory name two levels up from the Alamut variant file.
-l, --all Parse all variants without a genelist
-h, --help Show this message
##Selection of candidate genes