SNPSIFT

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.