java -jar snpEff.jar
[eff|ann] : Annotate variants / calculate effects (you can use either 'ann' or 'eff', they mean the same). Default: ann (no command or 'ann').
build : Build a SnpEff database.
buildNextProt : Build a SnpEff for NextProt (using NextProt's XML files).
cds : Compare CDS sequences calculated form a SnpEff database to the one in a FASTA file. Used for checking databases correctness.
closest : Annotate the closest genomic region.
count : Count how many intervals (from a BAM, BED or VCF file) overlap with each genomic interval.
databases : Show currently available databases (from local config file).
download : Download a SnpEff database.
dump : Dump to STDOUT a SnpEff database (mostly used for debugging).
genes2bed : Create a bed file from a genes list.
len : Calculate total genomic length for each marker type.
protein : Compare protein sequences calculated form a SnpEff database to the one in a FASTA file. Used for checking databases correctness.
spliceAnalysis : Perform an analysis of splice sites. Experimental feature.
-c , -config : Specify config file
-d , -debug : Debug mode (very verbose).
-dataDir : Override data_dir parameter from config file.
-download : Download a SnpEff database, if not available locally. Default: true
-nodownload : Do not download a SnpEff database, if not available locally.
-noShiftHgvs : Do not shift variants towards most 3-prime position (as required by HGVS).
-h , -help : Show this help and exit
-noLog : Do not report usage statistics to server
-t : Use multiple threads (implies '-noStats'). Default 'off'
-q , -quiet : Quiet mode (do not show any messages or errors)
-v , -verbose : Verbose mode
-canon : Only use canonical transcripts.
-interval : Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times)
-motif : Annotate using motifs (requires Motif database).
-nextProt : Annotate using NextProt (requires NextProt database).
-noGenome : Do not load any genomic database (e.g. annotate using custom files).
-noMotif : Disable motif annotations.
-noNextProt : Disable NextProt annotations.
-onlyReg : Only use regulation tracks.
-onlyProtein : Only use protein coding transcripts. Default: false
-onlyTr : Only use the transcripts in this file. Format: One transcript ID per line.
-reg : Regulation track to use (this option can be used add several times).
-ss , -spliceSiteSize : Set size for splice sites (donor and acceptor) in bases. Default: 2
-strict : Only use 'validated' transcripts (i.e. sequence has been checked). Default: false