Package org.snpsift
package org.snpsift
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ClassDescriptionGeneric SnpSift tool callerConvert VCf file to allele matrix Note: Only use SNPs Note: Only variants with two possible alleles.Annotate a VCF file with ID from another VCF file (database)Count number of cases and controlsCalculate genotyping concordance between two VCF files.Convert allele 'matrix' file into Covariance matrix Note: Only variants with two possible alleles.Annotate a VCF file with dbNSFP.Extract fields from VCF file to a TXT (tab separated) formatGeneric SnpSift filter Filter out data based on VCF attributes: - Chromosome, Position, etc.Filter using CHROM:POS onlyGeneric SnpSift genotype filter Removes genotypes matching the filter: e.g.Annotate a VCF file using Gene sets (MSigDb) or gene ontology (GO)Add genotype information to INFO fieldsAnnotate a VCF file using GWAS catalog database Loads GWAS catalog in memory, thus it makes no assumption about order.Intersect intervalsFilter variants that hit intervalsFilter variants that hit intervals Use an indexed VCF file.Annotate a VCF file with ID from another VCF file (database)Draws a pedigree using SVG according to a VCF fileAnnotate using PhastCons score filesAnnotate if a variant is 'private'.Removes reference genotypes.Removes INFO fieldsSort VCF file/s by chromosome invalid input: '&' positionSplit a large VCF file by chromosome or bby number of linesCalculate Ts/Tv rations per sample (transitions vs transversions)Annotate a VCF file with variant typeTransform a VCF to a TPED fileCheck VCF files (run some simple checks)Annotate a field based on an operation (max, min, etc.) of other VCF fieldsCalculate 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.