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 TypeClassDescriptionclassConvert VCf file to allele matrix Note: Only use SNPs Note: Only variants with two possible alleles.classAnnotate a VCF file with ID from another VCF file (database)classAnnotate a VCF file from another VCF file (database) The database file is loaded into memory.classCount number of cases and controlsclassCalculate genotyping concordance between two VCF files.classConvert allele 'matrix' file into Covariance matrix Note: Only variants with two possible alleles.classAnnotate a VCF file with dbNSFP.classExtract fields from VCF file to a TXT (tab separated) formatclassGeneric SnpSift filter Filter out data based on VCF attributes: - Chromosome, Position, etc.classFilter using CHROM:POS onlyclassGeneric SnpSift genotype filter Removes genotypes matching the filter: e.g.classAnnotate a VCF file using Gene sets (MSigDb) or gene ontology (GO)classAdd genotype information to INFO fieldsclassAnnotate a VCF file using GWAS catalog database Loads GWAS catalog in memory, thus it makes no assumption about order.classIntersect intervalsclassFilter variants that hit intervalsclassFilter variants that hit intervals Use an indexed VCF file.classAnnotate a VCF file with ID from another VCF file (database)classDraws a pedigree using SVG according to a VCF fileclassAnnotate using PhastCons score filesclassAnnotate if a variant is 'private'.classRemoves reference genotypes.classRemoves INFO fieldsclassSort VCF file/s by chromosome invalid input: '&' positionclassSplit a large VCF file by chromosome or bby number of linesclassCalculate Ts/Tv rations per sample (transitions vs transversions)classAnnotate a VCF file with variant typeclassTransform a VCF to a TPED fileclassCheck VCF files (run some simple checks)classAnnotate 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 TypeClassDescriptionclassSummarize a VCF annotated file -
Uses of SnpSift in org.snpsift.hwe
Subclasses of SnpSift in org.snpsift.hweModifier and TypeClassDescriptionclassCalculate Hardy-Weinberg equilibrium and goodness of fit for each entry in a VCF file