SNPSIFT(1)

📦 version 5.4.b, in debian bookworm, debian trixie, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 NAME 💖

okay so bestie, meet snpSift — she's literally a tool to annotate and manipulate genome variants 🧬✨ no cap, that's the whole vibe.

🌸 SYNOPSIS 🌸

like, you give her a [command], maybe some [options], maybe some [files], and she goes off 💅

🎀 AVAILABLE COMMANDS 🎀

so these are all the little side quests she can run for you 👑

  • alleleMat — Create an allele matrix output. ✨
  • annotate — Annotate 'ID' from a database (e.g. dbSnp). Assumes entries are sorted. 🫶
  • caseControl — Compare how many variants are in 'case' and in 'control' groups; calculate p-values. 📊
  • ccs — Case control summary. Case and control summaries by region, allele frequency and variant's functional effect. 💜
  • concordance — Concordance metrics between two VCF files. 🦋
  • covMat — Create an covariance matrix output (allele matrix as input). 🌈
  • dbnsfp — Annotate with multiple entries from dbNSFP. 🍓
  • extractFields — Extract fields from VCF file into tab separated format. 📋
  • filter — Filter using arbitrary expressions. 🔥
  • geneSets — Annotate using MSigDb gene sets (MSigDb includes: GO, KEGG, Reactome, BioCarta, etc.) 🧚
  • gt — Add Genotype to INFO fields and remove genotype fields when possible. 💅
  • gtfilter — Filter genotype using arbitrary expressions. ✂️
  • gwasCat — Annotate using GWAS catalog. 📚
  • hwe — Calculate Hardy-Weimberg parameters and perform a godness of fit test. 📈
  • intersect — Intersect intervals (genomic regions). 🎯
  • intervals — Keep variants that intersect with intervals. 💖
  • intIdx — Keep variants that intersect with intervals. Index-based method: Used for large VCF file and a few intervals to retrieve. 🏎️
  • join — Join files by genomic region. 🤝
  • op — Annotate using an operator. ➕
  • phastCons — Annotate using conservation scores (phastCons). 🌿
  • private — Annotate if a variant is private to a family or group. 🙈
  • rmRefGen — Remove reference genotypes. 🗑️
  • rmInfo — Remove INFO fields. ✂️
  • sort — Sort VCF file/s (if multiple input VCFs, merge and sort). 🔤
  • split — Split VCF by chromosome. 🧩
  • tstv — Calculate transition to transversion ratio. 🔄
  • varType — Annotate variant type (SNP,MNP,INS,DEL or MIXED). 🏷️
  • vcfCheck — Check that VCF file is well formed. ✅
  • vcf2tped — Convert VCF to TP. 🌀
ngl, some of these got squished together in the original scroll, but we rescued every single one, bestie. nothing left behind 💀

💅 OPTIONS 💅

🌈 Generic options

the universal settings, the main character switches fr fr:

  • -c, -config — Specify config file. Default: ~/.snpEff/snpEff.config 🛠️
  • -d, -debug — Debug mode. 🐛
  • -db <file>, -database <file> — Database file name (for commands that require databases). 🗄️
  • -configOption name=value — Override a config file option. 🎛️
  • -download — Download a SnpEff database, if not available locally. Default: true ⬇️
  • -g <name>, -genome <name> — Genome version (for commands that require databases). 🧬
  • -nodownload — Do not download a SnpEff database, if not available locally. 🚫
  • -noLog — Do not report usage statistics to server. 🤫
  • -h, -help — Show this help and exit. ❓
  • -v, -verbose — Verbose mode. 🗣️
  • -version — Show version number and exit. 🔢

🦋 SEE ALSO 🦋

👑 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. 🙏

okay that's the whole page, and it's giving iconic 💖 this came to you from snpSift, dated February 2022 — that's the source and the date, and honestly? slay. bye bestie, go annotate something 🎀✨

📦 where this page comes from