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 <[email protected]> from the Debian project, but may be used by others. Please report possibly missing or misleading information.