Package picard.vcf
package picard.vcf
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ClassDescriptionCombines multiple Variant Calling Metrics files into a single file.Takes a VCFFileReader and an IntervalList and provides a single iterator over all variants in all the intervals.Collects variants and generates metrics about them.Collects summary and per-sample metrics about variant calls in a VCF file.A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.A collection of metrics relating to snps and indels within a variant-calling file (VCF).Tool for replacing or fixing up a VCF header.The scheme is defined in the constructor.The default scheme is derived from the GA4GH Benchmarking Work Group's proposed evaluation scheme.Simple little class that combines multiple VCFs that have exactly the same set of samples and nonoverlapping sets of loci.SummaryA simple structure to return the results of getAlleles.Class that holds metrics about the Genotype Concordance contingency tables.A class to store the counts for various truth and call state classifications relative to a reference.Class that holds detail metrics about Genotype ConcordanceThis defines for each valid TruthState and CallState tuple, the set of contingency table entries that to which the tuple should contribute.Created by kbergin on 6/19/15.Created by kbergin on 7/30/15.A class to store the various classifications for: 1.These states represent the relationship between the call genotype and the truth genotype relative to a reference sequence.A specific state for a 2x2 contingency table.A minute class to store the truth and call state respectively.These states represent the relationship between a truth genotype and the reference sequence.Class that holds summary metrics about Genotype ConcordanceAn accumulator for collecting metrics about a single-sample GVCF.SummaryCreates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.Creates a TSV from sample name to VCF/GVCF path, with one line per input.Combines multiple variant files into a single variant file.An iterator that takes a pair of iterators over VariantContexts and iterates over them in tandem.Little class to hold a pair of VariantContexts that are in sync with one another.Renames a sample within a VCF or BCF.Sorts one or more VCF files according to the order of the contigs in the header/sequence dictionary and then by coordinate.Splits the input VCF file into two, one for indels and one for SNPs.Takes a VCF file and a Sequence Dictionary (from a variety of file types) and updates the Sequence Dictionary in VCF.Converts an ASCII VCF file to a binary BCF or vice versa.Converts a VCF or BCF file to a Picard Interval List.Created by farjoun on 4/1/17.