The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at


Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,127 admin
edited September 2012 in GenomeSTRiP Documentation

1. Introduction

The VariantsPerSample annotator is invoked through the SVVariantAnnotator walker, which defines arguments common to all annotators.

The VariantsPerSample annotator is a simple annotator that counts how many variants are in each sampled genome. The output can be rolled up into population level statistics.

In the current implementation, VariantsPerSample uses the GSSAMPLES INFO tag in the input VCF file to determine which samples carry the variant. The input VCF file should not contain genotypes.

Filtered variants are not counted in the totals.

2. Inputs / Arguments

  • -populationMap <map-file> : A tab-delimited input file containing two
    columns: the sample ID and a population ID for that sample. If supplied, the
    population information will be carried over into the output report.

3. Annotations

No VCF annotations are produced, but this annotator is used to produce a
report file. The report file will contain one line per sample. The report
includes the number of variants and also the population if -populationMap is

4. Example

java -Xmx2g -cp SVToolkit.jar:GenomeAnalysisTK.jar \
    org.broadinstitute.sting.gatk.CommandLineGATK \ 
    -T SVVariantAnnotator \ 
    -A VariantsPerSample \ 
    -R /humgen/1kg/reference/human_g1k_v37.fasta \ 
    -BTI variant \ 
    -B:variant,VCF input.vcf \ 
    -populationMap \
    -writeReport \ 
    -reportFile variants_per_sample.dat
Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

Sign In or Register to comment.