NonVariantAnnotator

Annotator used to detect and filter sites that are likely not polymorphic in the genotyped population.

Category: Variant Annotators

The NonVariant annotator is invoked through the SVAnnotator framework, which defines arguments common to all annotators.

Introduction

The NonVariant annotator computes a "non-variance" score for each site in the input VCF. Only sites that have all homozygous reference genotype calls receive a numeric score. For sites with all homozygous reference genotypes, the non-variance score is the minimum quality score (either GQ or CNQ, depending on the variant) across all evaluated samples. A higher non-variance score indicates higher confidence that no sample in the evaluated population has a polymorphism at this site.

If genotype filters are present in the input VCF, they will be used by default and the corresponding genotypes will not be used in computing the non-variance score, except that genotypes failing only the "LQ" filter, which is based on the genotype quality values, are always used.

The -sample argument can be used to restrict the non-variance test to a subset of the samples in the input VCF.

Output Formats

This annotator can produce the following outputs: annotated VCF, report file.

The following VCF annotations are produced by this annotator (and corresponding columns in the report file):

GSNONVARSCORE

The non-variance score. For uniformly homozygous reference sites, the minimum genotype quality.

Example

 java -Xmx4g -cp SVToolkit.jar \
     org.broadinstitute.sv.main.SVAnnotator \
     -A NonVariant \
     -R human_g1k_v37.fasta \
     -vcf input.vcf \
     -O output.vcf \
     -writeReport true \
     -reportDirectory reportdir

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NonVariantAnnotator specific arguments

Name	Type	Default value	Summary
Optional Parameters
-filterGenotypes	Boolean	true	True to ignore genotypes that have been filtered. The "LQ" filter is always respected, however.
-filterVariants	Boolean	true	True to ignore variants that have been filtered
-genderMapFile	List[File]	NA	Map file(s) containing the gender for each sample
-ploidyMapFile	File	NA	Map file containing ploidy information
-sample	List[String]	NA	Sample(s) or .list file of sample names to be evaluated

Argument details