Package org.snpeff.snpEffect.commandLine

Interface Summary

Interface	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(); }

Class Summary

Class	Description
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
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

Enum Summary

Enum	Description
SnpEffCmdDump.DumpFormat