VariantsPerSampleAnnotator

Annotator that reports on the distribution of variant calls across samples.

Category: Variant Annotators

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

Introduction

The VariantsPerSample annotator reports the distribution of variant calls across samples. It reports both total variants in each sample and the number of singletons.

Input Formats

Population map files are tab delimited files with two columns. The first column specifies the sample identifier and the second column specifies a population identifier. A header line is optional, but if present the column names should be SAMPLE and POPULATION.

Output Formats

This annotator can produce the following outputs: report file.

The report file contains one line per sample, with the following columns:

SAMPLE

The sample identifier.

POPULATION

The population for this sample.

This column is emitted as a convenience, but the population map is not othewise used by this annotator.

VARIANTS

The number of sites called variant for this sample.

Specifically, the number of sites where the sample carries at least one non-reference allele.

SINGLETONS

The number of singleton sites, sites where this sample is the only variant sample in the evaluated cohort.

Example

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

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VariantsPerSampleAnnotator specific arguments

Name	Type	Default value	Summary
Optional Parameters
-filterGenotypes	String	NA	True to ignore genotypes that have been filtered (default true)
-filterVariants	String	NA	True to ignore variants that have been filtered (default true)
-genotypeQualityThreshold	Double	NA	Ignore genotypes below this genotype quality GQ/CNQ value (default no threshold)
-populationMapFile	List[File]	NA	Map file (or files) containing sample to population assignments
-sample	List[String]	NA	Sample(s) or .list file of sample names. If specified, only the listed samples will be used to evaluate the variants.

Argument details