# Package org.snpeff.snpEffect.commandLine

package org.snpeff.snpEffect.commandLine

Related Packages
Package
Description
org.snpeff.snpEffect
org.snpeff.snpEffect.factory
Class
Description
CommandLine
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(); }
SnpEffCmdAcat
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.
SnpEffCmdBuild
Command line program: Build database
SnpEffCmdBuildNextProt
Parse NetxProt XML file and build a database http://www.nextprot.org/
SnpEffCmdCds
Command line: Calculate coding sequences from a file and compare them to the ones calculated from our data structures
SnpEffCmdClosest
Command line: Find closes marker to each variant
SnpEffCmdCount
Count reads from a BAM file given a list of intervals
SnpEffCmdDatabases
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
SnpEffCmdDownload
Command line program: Download and install a (pre built) database
SnpEffCmdDump
Command line program: Build database
SnpEffCmdDump.DumpFormat
SnpEffCmdEff
Command line program: Predict variant effects
SnpEffCmdGenes2Bed
Simple test program
SnpEffCmdGsa
Command line: Gene-Sets Analysis Perform gene set analysys
SnpEffCmdLen
Calculate the maximum interval length by type, for all markers in a genome
SnpEffCmdPdb
PDB distance analysis
SnpEffCmdProtein
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.
SnpEffCmdSeq
Command line program: Show a transcript or a gene
SnpEffCmdShow
Command line program: Show a transcript or a gene
SnpEffCmdTranslocationsReport
Create an SVG representation of a Marker