SNPEFF(1)

💖 snpEff(1) — the genetic variant annotation & effect prediction toolbox 💖

okay bestie, sit down, hydrate, and let me tell you about snpEff. It's a genetic variant annotation and effect prediction toolbox, and honestly? It's giving main character energy for your whole variant-calling pipeline. ✨

🌸 SYNOPSIS 🌸

snpEff [command] [options] [files]

That's it. That's the whole shape of it: you pick a command, you throw in some options, you point it at some files, and she goes. 🦋

👑 AVAILABLE COMMANDS 👑

Every single one of these is a legit thing you can ask snpEff to do. No skips, no shortcuts, we're doing all of them:

• [err|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 from 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.
• pdb — Build interaction database (based on PDB data).
• protein — Compare protein sequences calculated from a SnpEff database to the one in a FASTA file. Used for checking databases correctness.
• seq — Show sequence (from command line) translation.
• show — Show a text representation of genes or transcripts coordinates, DNA sequence and protein sequence.
• translocReport — Create a translocations report (from VCF file).

Sixteen commands. Sixteen! We love a multi-talented icon. 💅

✨ OPTIONS ✨

🎀 Generic options

The everyday fits-and-starts, the little quality-of-life levers:

• -c , -config — Specify config file. Default: ~/.snpEff/snpEff.config
• -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
• -t — Use multiple threads (implies '-noStats'). Default 'off'
• -q , -quiet — Quiet mode (do not show any messages or errors)
• -v , -verbose — Verbose mode
• -version — Show version number and exit

ngl, -q and -v are enemies. Pick a lane bestie. 😭

🧚 Database options

This is where the transcript-filtering, annotation-source and splice-site girlies live. Buckle up.

• -canon — Only use canonical transcripts.
• -canonList <file> — Only use canonical transcripts, replace some transcripts using the 'gene_id transcript_id' entries in <file>.
• -interaction — Annotate using interactions (requires interaction database). Default: true
• -interval <file> — Use a custom interval 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 interaction 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)

🫶 notice how -interval and -reg are both "use this as many times as you want" options? Stack them. Go feral.

🔥 SEE ALSO 🔥

The lore, the backstory, the extended universe:

• https://pcingola.github.io/SnpEff/se_introduction/

💜 AUTHOR 💜

This manual page was written by Pierre Gruet <pgt@debian.org> from the Debian project, but may be used by others. Please report possibly missing or misleading information.

And that's the whole page, bestie — snpEff, manual section 1, last touched February 2021. Iconic then, iconic now. Go annotate something. 👑✨