---
name: "snpSift"
section: "1"
platform: "linux"
package: "snpsift"
version: "5.2.e+dfsg-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/snpSift"
---

# snpSift(1)

tool to annotate and manipulate genome variants

## NAME

snpSift - tool to annotate and manipulate genome variants

## SYNOPSIS

**snpSift** \[*command*\] \[*options*\] \[*files*\]

## AVAILABLE COMMANDS

- **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

  ## OPTIONS

### Generic options

- **-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

**https://pcingola.github.io/SnpEff/se\_introduction/**

**snpeff**(1)

## 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.