Category

Genome Variant Analysis


Usage

java -jar snpEff.jar


Manual

[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


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