# Uses of Class
org.snpsift.SnpSift

Packages that use SnpSift
Package
Description
org.snpsift
org.snpsift.caseControl
org.snpsift.hwe

## Uses of SnpSift in org.snpsift

Subclasses of SnpSift in org.snpsift
Modifier and Type
Class
Description
`class`
`SnpSiftCmdAlleleMatrix`
Convert VCf file to allele matrix Note: Only use SNPs Note: Only variants with two possible alleles.
`class`
`SnpSiftCmdAnnotate`
Annotate a VCF file with ID from another VCF file (database)
`class`
`SnpSiftCmdAnnotateMem`
Annotate a VCF file from another VCF file (database) The database file is loaded into memory.
`class`
`SnpSiftCmdCaseControl`
Count number of cases and controls
`class`
`SnpSiftCmdConcordance`
Calculate genotyping concordance between two VCF files.
`class`
`SnpSiftCmdCovarianceMatrix`
Convert allele 'matrix' file into Covariance matrix Note: Only variants with two possible alleles.
`class`
`SnpSiftCmdDbNsfp`
Annotate a VCF file with dbNSFP.
`class`
`SnpSiftCmdExtractFields`
Extract fields from VCF file to a TXT (tab separated) format
`class`
`SnpSiftCmdFilter`
Generic SnpSift filter Filter out data based on VCF attributes: - Chromosome, Position, etc.
`class`
`SnpSiftCmdFilterChrPos`
Filter using CHROM:POS only
`class`
`SnpSiftCmdFilterGt`
Generic SnpSift genotype filter Removes genotypes matching the filter: e.g.
`class`
`SnpSiftCmdGeneSets`
Annotate a VCF file using Gene sets (MSigDb) or gene ontology (GO)
`class`
`SnpSiftCmdGt`
Add genotype information to INFO fields
`class`
`SnpSiftCmdGwasCatalog`
Annotate a VCF file using GWAS catalog database Loads GWAS catalog in memory, thus it makes no assumption about order.
`class`
`SnpSiftCmdIntersect`
Intersect intervals
`class`
`SnpSiftCmdIntervals`
Filter variants that hit intervals
`class`
`SnpSiftCmdIntervalsIndex`
Filter variants that hit intervals Use an indexed VCF file.
`class`
`SnpSiftCmdJoin`
Annotate a VCF file with ID from another VCF file (database)
`class`
`SnpSiftCmdPedShow`
Draws a pedigree using SVG according to a VCF file
`class`
`SnpSiftCmdPhastCons`
Annotate using PhastCons score files
`class`
`SnpSiftCmdPrivate`
Annotate if a variant is 'private'.
`class`
`SnpSiftCmdRemoveReferenceGenotypes`
Removes reference genotypes.
`class`
`SnpSiftCmdRmInfo`
Removes INFO fields
`class`
`SnpSiftCmdSort`
Sort VCF file/s by chromosome invalid input: '&' position
`class`
`SnpSiftCmdSplit`
Split a large VCF file by chromosome or bby number of lines
`class`
`SnpSiftCmdTsTv`
Calculate Ts/Tv rations per sample (transitions vs transversions)
`class`
`SnpSiftCmdVarType`
Annotate a VCF file with variant type
`class`
`SnpSiftCmdVcf2Tped`
Transform a VCF to a TPED file
`class`
`SnpSiftCmdVcfCheck`
Check VCF files (run some simple checks)
`class`
`SnpSiftCmdVcfOperator`
Annotate a field based on an operation (max, min, etc.) of other VCF fields
Methods in org.snpsift that return SnpSift
Modifier and Type
Method
Description
`SnpSift`
SnpSift.`cmd()`
Run: Executes the appropriate class

## Uses of SnpSift in org.snpsift.caseControl

Subclasses of SnpSift in org.snpsift.caseControl
Modifier and Type
Class
Description
`class`
`SnpSiftCmdCaseControlSummary`
Summarize a VCF annotated file

## Uses of SnpSift in org.snpsift.hwe

Subclasses of SnpSift in org.snpsift.hwe
Modifier and Type
Class
Description
`class`
`SnpSiftCmdHwe`
Calculate Hardy-Weinberg equilibrium and goodness of fit for each entry in a VCF file