Package org.snpeff.snpEffect.commandLine


package org.snpeff.snpEffect.commandLine
  • Class
    Description
    Command line and arguments The way to run a command from 'main' is usually: public static void main(String[] args) { Command cmd = new Command(); cmd.parseArgs(args); cmd.run(); }
    ACAT: Create ACAT score for T2D project Note: This is just used to compile 'ACAT' score in T2D-GENES project, not useful at all for general audience.
    Command line program: Build database
    Parse NetxProt XML file and build a database http://www.nextprot.org/
    Command line: Calculate coding sequences from a file and compare them to the ones calculated from our data structures
    Command line: Find closes marker to each variant
    Count reads from a BAM file given a list of intervals
    Show all databases configures in snpEff.config Create an HTML 'download' table based on the config file Also creates a list of genome for Galaxy menu
    Command line program: Download and install a (pre built) database
    Command line program: Build database
     
    Command line program: Predict variant effects
    Simple test program
    Command line: Gene-Sets Analysis Perform gene set analysys
    Calculate the maximum interval length by type, for all markers in a genome
    PDB distance analysis
    Command line: Read protein sequences from a file and compare them to the ones calculated from our data structures Note: This is done in order to see potential incompatibility errors between genome sequence and annotation.
    Command line program: Show a transcript or a gene
    Command line program: Show a transcript or a gene
    Create an SVG representation of a Marker