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.