Uses of Class
org.snpsift.SnpSift
Packages that use SnpSift
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Uses of SnpSift in org.snpsift
Subclasses of SnpSift in org.snpsiftModifier and TypeClassDescriptionclass
Convert VCf file to allele matrix Note: Only use SNPs Note: Only variants with two possible alleles.class
Annotate a VCF file with ID from another VCF file (database)class
Count number of cases and controlsclass
Calculate genotyping concordance between two VCF files.class
Convert allele 'matrix' file into Covariance matrix Note: Only variants with two possible alleles.class
Annotate a VCF file with dbNSFP.class
Extract fields from VCF file to a TXT (tab separated) formatclass
Generic SnpSift filter Filter out data based on VCF attributes: - Chromosome, Position, etc.class
Filter using CHROM:POS onlyclass
Generic SnpSift genotype filter Removes genotypes matching the filter: e.g.class
Annotate a VCF file using Gene sets (MSigDb) or gene ontology (GO)class
Add genotype information to INFO fieldsclass
Annotate a VCF file using GWAS catalog database Loads GWAS catalog in memory, thus it makes no assumption about order.class
Intersect intervalsclass
Filter variants that hit intervalsclass
Filter variants that hit intervals Use an indexed VCF file.class
Annotate a VCF file with ID from another VCF file (database)class
Draws a pedigree using SVG according to a VCF fileclass
Annotate using PhastCons score filesclass
Annotate if a variant is 'private'.class
Removes reference genotypes.class
Removes INFO fieldsclass
Sort VCF file/s by chromosome invalid input: '&' positionclass
Split a large VCF file by chromosome or bby number of linesclass
Calculate Ts/Tv rations per sample (transitions vs transversions)class
Annotate a VCF file with variant typeclass
Transform a VCF to a TPED fileclass
Check VCF files (run some simple checks)class
Annotate a field based on an operation (max, min, etc.) of other VCF fieldsMethods in org.snpsift that return SnpSift -
Uses of SnpSift in org.snpsift.caseControl
Subclasses of SnpSift in org.snpsift.caseControlModifier and TypeClassDescriptionclass
Summarize a VCF annotated file -
Uses of SnpSift in org.snpsift.hwe
Subclasses of SnpSift in org.snpsift.hweModifier and TypeClassDescriptionclass
Calculate Hardy-Weinberg equilibrium and goodness of fit for each entry in a VCF file