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.
The VariantsPerSample annotator reports the distribution of variant calls across samples. It reports both total variants in each sample and the number of singletons.
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.
This annotator can produce the following outputs: report file.
The report file contains one line per sample, with the following columns:
- The sample identifier.
- The population for this sample.
- This column is emitted as a convenience, but the population map is not othewise used by this annotator.
- The number of sites called variant for this sample.
- Specifically, the number of sites where the sample carries at least one non-reference allele.
- The number of singleton sites, sites where this sample is the only variant sample in the evaluated cohort.
java -Xmx4g -cp SVToolkit.jar \ org.broadinstitute.sv.main.SVAnnotator \ -A VariantsPerSample \ -R human_g1k_v37.fasta \ -vcf input.vcf \ -writeReport true \ -reportDirectory reportdir
VariantsPerSampleAnnotator specific arguments
|-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.|
True to ignore genotypes that have been filtered (default true).
True to ignore variants that have been filtered (default true).
Ignore genotypes below this genotype quality GQ/CNQ value (default no threshold).
Map file (or files) containing sample to population assignments.
Sample(s) or .list file of sample names. If specified, only the listed samples will be used to evaluate the variants..