# Uses of Interface
org.snpeff.snpEffect.commandLine.CommandLine

Packages that use CommandLine
Package
Description
org.snpeff
org.snpeff.fastq
org.snpeff.snpEffect
org.snpeff.snpEffect.commandLine
org.snpeff.spliceSites

## Uses of CommandLine in org.snpeff

Classes in org.snpeff that implement CommandLine
Modifier and Type
Class
Description
`class`
`SnpEff`
SnpEff's main command line program

## Uses of CommandLine in org.snpeff.fastq

Classes in org.snpeff.fastq that implement CommandLine
Modifier and Type
Class
Description
`class`
`FastqSplit`
Split a fastq into N files

## Uses of CommandLine in org.snpeff.snpEffect

Subinterfaces of CommandLine in org.snpeff.snpEffect
Modifier and Type
Interface
Description
`interface`
`VcfAnnotator`
Annotate a VCF file: E.g.
Classes in org.snpeff.snpEffect that implement CommandLine
Modifier and Type
Class
Description
`class`
`VcfAnnotatorChain`
Maintains a list of VcfAnnotators and applies them one by one in the specified order

## Uses of CommandLine in org.snpeff.snpEffect.commandLine

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

## Uses of CommandLine in org.snpeff.spliceSites

Classes in org.snpeff.spliceSites that implement CommandLine
Modifier and Type
Class
Description
`class`
`SnpEffCmdSpliceAnalysis`
Analyze sequences from splice sites