Uses of Class
org.snpeff.SnpEff
Packages that use SnpEff
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Uses of SnpEff in org.snpeff
Fields in org.snpeff declared as SnpEffMethods in org.snpeff that return SnpEffMethods in org.snpeff with parameters of type SnpEffModifier and TypeMethodDescriptionprotected boolean
SnpEff.run
(SnpEff snpEff, String[] args, StringBuilder err) Run a SnpEff (usually a sub-class) -
Uses of SnpEff in org.snpeff.snpEffect.commandLine
Subclasses of SnpEff in org.snpeff.snpEffect.commandLineModifier and TypeClassDescriptionclass
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
Command line program: Build databaseclass
Parse NetxProt XML file and build a database http://www.nextprot.org/class
Command line: Calculate coding sequences from a file and compare them to the ones calculated from our data structuresclass
Command line: Find closes marker to each variantclass
Count reads from a BAM file given a list of intervalsclass
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 menuclass
Command line program: Download and install a (pre built) databaseclass
Command line program: Build databaseclass
Command line program: Predict variant effectsclass
Simple test programclass
Command line: Gene-Sets Analysis Perform gene set analysysclass
Calculate the maximum interval length by type, for all markers in a genomeclass
PDB distance analysisclass
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
Command line program: Show a transcript or a geneclass
Command line program: Show a transcript or a geneclass
Create an SVG representation of a Marker -
Uses of SnpEff in org.snpeff.spliceSites
Subclasses of SnpEff in org.snpeff.spliceSitesModifier and TypeClassDescriptionclass
Analyze sequences from splice sites