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.
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SnpEffCmdBuild |
Command line program: Build database
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SnpEffCmdBuildNextProt |
Parse NetxProt XML file and build a database
http://www.nextprot.org/
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SnpEffCmdCds |
Command line: Calculate coding 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.
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SnpEffCmdClosest |
Command line: Find closes marker to each variant
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SnpEffCmdCount |
Count reads from a BAM file given a list of intervals
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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
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SnpEffCmdDownload |
Command line program: Build database
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SnpEffCmdDump |
Command line program: Build database
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SnpEffCmdEff |
Command line program: Predict variant effects
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SnpEffCmdGenes2Bed |
Simple test program
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SnpEffCmdGsa |
Command line: Gene-Sets Analysis
Perform gene set analysys
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SnpEffCmdLen |
Calculate the maximum interval length by type, for all markers in a genome
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SnpEffCmdPdb |
PDB distance analysis
References: http://biojava.org/wiki/BioJava:CookBook:PDB:read
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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.
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SnpEffCmdSeq |
Command line program: Show a transcript or a gene
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SnpEffCmdShow |
Command line program: Show a transcript or a gene
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SnpEffCmdTranslocationsReport |
Create an SVG representation of a Marker
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