snpSift - tool to annotate and manipulate genome variants

       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.

snpSift                                           February 2022                                       SNPSIFT(1)

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
              Keepvariantsthatintersectwithintervals.  intIdx

       Keepvariantsthatintersectwithintervals.Index-basedmethod:UsedforlargeVCFfileandafewintervalstoretrieve
              join

       Joinfilesbygenomicregion.
              op

       Annotateusinganoperator.
              phastCons

       Annotateusingconservationscores(phastCons).
              private

       Annotateifavariantisprivatetoafamilyorgroup.
              rmRefGen

       Removereferencegenotypes.
              rmInfo

       RemoveINFOfields.
              sort

       SortVCFfile/s(ifmultipleinputVCFs,mergeandsort).
              split

       SplitVCFbychromosome.
              tstv

       Calculatetransitiontotransversionratio.
              varType

       Annotatevarianttype(SNP,MNP,INS,DELorMIXED).
              vcfCheck

       CheckthatVCFfileiswellformed.
              vcf2tped

       Convert VCF to TP

       snpSift - tool to annotate and manipulate genome variants

Genericoptions-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

https://pcingola.github.io/SnpEff/se_introduction/snpeff(1)

snpSift [command] [options] [files]