snpEff version SnpEff 5.2f (build 2025-02-07 08:36), by Pablo Cingolani
Usage: snpEff [ann] [options] genome_version [input_file]


	variants_file                   : Default is STDIN



Options:
	-chr <string>                   : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
	-classic                        : Use old style annotations instead of Sequence Ontology and Hgvs.
	-csvStats <file>                : Create CSV summary file.
	-download                       : Download reference genome if not available. Default: true
	-i <format>                     : Input format [ vcf, bed ]. Default: VCF.
	-fileList                       : Input actually contains a list of files to process.
	-o <format>                     : Output format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
	-s , -stats, -htmlStats         : Create HTML summary file.  Default is 'snpEff_summary.html'
	-noStats                        : Do not create stats (summary) file

Results filter options:
	-fi , -filterInterval  <file>   : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
	-no-downstream                  : Do not show DOWNSTREAM changes
	-no-intergenic                  : Do not show INTERGENIC changes
	-no-intron                      : Do not show INTRON changes
	-no-upstream                    : Do not show UPSTREAM changes
	-no-utr                         : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
	-no <effectType>                : Do not show 'EffectType'. This option can be used several times.

Annotations options:
	-cancer                         : Perform 'cancer' comparisons (Somatic vs Germline). Default: false
	-cancerSamples <file>           : Two column TXT file defining 'oringinal \t derived' samples.
	-fastaProt <file>               : Create an output file containing the resulting protein sequences.
	-fastaProtNoRef                 : Do not add reference sequences to the output (only valid when -fastaProt). Default: false
	-formatEff                      : Use 'EFF' field compatible with older versions (instead of 'ANN').
	-geneId                         : Use gene ID instead of gene name (VCF output). Default: false
	-hgvs                           : Use HGVS annotations for amino acid sub-field. Default: true
	-hgvsOld                        : Use old HGVS notation. Default: false
	-hgvs1LetterAa                  : Use one letter Amino acid codes in HGVS notation. Default: false
	-hgvsTrId                       : Use transcript ID in HGVS notation. Default: false
	-lof                            : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
	-noHgvs                         : Do not add HGVS annotations.
	-noLof                          : Do not add LOF and NMD annotations.
	-noOut                          : Do not write the output resuts to STDOUT (maybe used for debugging).
	-noShiftHgvs                    : Do not shift variants according to HGVS notation (most 3prime end).
	-oicr                           : Add OICR tag in VCF file. Default: false
	-sequenceOntology               : Use Sequence Ontology terms. Default: true

Generic options:
	-c , -config                 : Specify config file
	-configOption name=value     : Override a config file option
	-d , -debug                  : Debug mode (very verbose).
	-dataDir <path>              : 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.
	-h , -help                   : Show this help and exit
	-noLog                       : Do not report usage statistics to server
	-q , -quiet                  : Quiet mode (do not show any messages or errors)
	-v , -verbose                : Verbose mode
	-version                     : Show version number and exit

Database options:
	-canon                       : Only use canonical transcripts.
	-canonList <file>            : Only use canonical transcripts, replace some transcripts using the 'gene_id 	 transcript_id' entries in <file>.
	-tag <tagName>               : Only use transcript having a tag 'tagName'. This option can be used multiple times.
	-notag <tagName>             : Filter out transcript having a tag 'tagName'. This option can be used multiple times.
	-interaction                 : Annotate using interactions (requires interaction database). Default: true
	-interval <file>             : Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times)
	-maxTSL <TSL_number>         : Only use transcripts having Transcript Support Level lower than <TSL_number>.
	-motif                       : Annotate using motifs (requires Motif database). Default: true
	-nextProt                    : Annotate using NextProt (requires NextProt database).
	-noGenome                    : Do not load any genomic database (e.g. annotate using custom files).
	-noExpandIUB                 : Disable IUB code expansion in input variants
	-noInteraction               : Disable inteaction annotations
	-noMotif                     : Disable motif annotations.
	-noNextProt                  : Disable NextProt annotations.
	-onlyReg                     : Only use regulation tracks.
	-onlyProtein                 : Only use protein coding transcripts. Default: false
	-onlyTr <file.txt>           : Only use the transcripts in this file. Format: One transcript ID per line.
	-reg <name>                  : Regulation track to use (this option can be used add several times).
	-ss , -spliceSiteSize <int>  : Set size for splice sites (donor and acceptor) in bases. Default: 2
	-spliceRegionExonSize <int>  : Set size for splice site region within exons. Default: 3 bases
	-spliceRegionIntronMin <int> : Set minimum number of bases for splice site region within intron. Default: 3 bases
	-spliceRegionIntronMax <int> : Set maximum number of bases for splice site region within intron. Default: 8 bases
	-strict                      : Only use 'validated' transcripts (i.e. sequence has been checked). Default: false
	-ud , -upDownStreamLen <int> : Set upstream downstream interval length (in bases)
