# Package org.snpsift

package org.snpsift

Related Packages
Package
Description
org.snpsift.annotate
org.snpsift.antlr
org.snpsift.caseControl
org.snpsift.fileIterator
org.snpsift.gwasCatalog
org.snpsift.hwe
org.snpsift.lang
org.snpsift.pedigree
org.snpsift.phatsCons
org.snpsift.util
Class
Description
SnpSift
Generic SnpSift tool caller
SnpSiftCmdAlleleMatrix
Convert VCf file to allele matrix Note: Only use SNPs Note: Only variants with two possible alleles.
SnpSiftCmdAnnotate
Annotate a VCF file with ID from another VCF file (database)
SnpSiftCmdAnnotateMem
Annotate a VCF file from another VCF file (database) The database file is loaded into memory.
SnpSiftCmdCaseControl
Count number of cases and controls
SnpSiftCmdConcordance
Calculate genotyping concordance between two VCF files.
SnpSiftCmdCovarianceMatrix
Convert allele 'matrix' file into Covariance matrix Note: Only variants with two possible alleles.
SnpSiftCmdDbNsfp
Annotate a VCF file with dbNSFP.
SnpSiftCmdExtractFields
Extract fields from VCF file to a TXT (tab separated) format
SnpSiftCmdFilter
Generic SnpSift filter Filter out data based on VCF attributes: - Chromosome, Position, etc.
SnpSiftCmdFilterChrPos
Filter using CHROM:POS only
SnpSiftCmdFilterGt
Generic SnpSift genotype filter Removes genotypes matching the filter: e.g.
SnpSiftCmdGeneSets
Annotate a VCF file using Gene sets (MSigDb) or gene ontology (GO)
SnpSiftCmdGt
Add genotype information to INFO fields
SnpSiftCmdGwasCatalog
Annotate a VCF file using GWAS catalog database Loads GWAS catalog in memory, thus it makes no assumption about order.
SnpSiftCmdIntersect
Intersect intervals
SnpSiftCmdIntervals
Filter variants that hit intervals
SnpSiftCmdIntervalsIndex
Filter variants that hit intervals Use an indexed VCF file.
SnpSiftCmdJoin
Annotate a VCF file with ID from another VCF file (database)
SnpSiftCmdPedShow
Draws a pedigree using SVG according to a VCF file
SnpSiftCmdPhastCons
Annotate using PhastCons score files
SnpSiftCmdPrivate
Annotate if a variant is 'private'.
SnpSiftCmdRemoveReferenceGenotypes
Removes reference genotypes.
SnpSiftCmdRmInfo
Removes INFO fields
SnpSiftCmdSort
Sort VCF file/s by chromosome invalid input: '&' position
SnpSiftCmdSplit
Split a large VCF file by chromosome or bby number of lines
SnpSiftCmdTsTv
Calculate Ts/Tv rations per sample (transitions vs transversions)
SnpSiftCmdVarType
Annotate a VCF file with variant type
SnpSiftCmdVcf2Tped
Transform a VCF to a TPED file
SnpSiftCmdVcf2Tped.UseMissing
SnpSiftCmdVcfCheck
Check VCF files (run some simple checks)
SnpSiftCmdVcfOperator
Annotate a field based on an operation (max, min, etc.) of other VCF fields
SnpSiftCmdVcfOperator.Operator
VcfLd
Calculate Linkage Disequilibrium Reference: "Principles of population genetics (4th edition)" Hartl invalid input: '&' Clark, pages 73 to 81 Note: I try to follow the same notation as the book.