Package picard.vcf

Class GvcfMetricAccumulator

java.lang.Object
picard.vcf.CallingMetricAccumulator
picard.vcf.GvcfMetricAccumulator
All Implemented Interfaces:
VariantProcessor.Accumulator<CallingMetricAccumulator.Result>

public class GvcfMetricAccumulator extends CallingMetricAccumulator
An accumulator for collecting metrics about a single-sample GVCF. The main point here is to subset the context of each VariantContext as it comes by to the alleles present in the genotype of the only sample. Since this is a GVCF we expect a symbolic \invalid input: '<'NON_REF\> allele to be present in each VC. If we do not subset the context this symbolic allele will cause the regular CallingMetricAccumulator to return only a small subset of the relevant metrics.