Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,434Administrator, GATK Dev admin
edited September 2012 in GenomeSTRiP Documentation

1. Introduction

The PlotGenotypingResults utility produces plots that help to visualize the
genotyping data for individual sites.

The plots show a histogram of read depth, decorated with information about
aberrant read pairs and/or breakpoint spanning reads and showing the called
genotype for each sample. This utility requires information from auxilliary
data files produced during genotyping which are written to the genotyping run

2. Inputs / Arguments

  • -site <site-list> : The ID of a genotyped site (required). This should
    match the third column in the output vcf file. This argument can be supplied
    multiple times. It can also be a comma-separated list of sites or a file (with
    extension .list) containing a list of sites, one site per line.

  • -runDirectory <dir> : The run directory from a genotyping run which
    contains the auxilliary output files. This is the typical way to specify the
    location of the auxilliary output files.

  • -partitionMapFile <file> : Full path to the partition map file that maps
    site IDs to the partition used during genotyping (when genotyping is run in
    parallel). The default value is in the specified
    run directory. If you did not use parallel genotyping, you need to supply
    -auxFilePrefix instead.

  • -auxFilePrefix <string> : The path prefix to the auxilliary output files
    for the listed sites. This is the part of the path without the suffixes such
    as .genotypes.vcf or .genotypes.gts.dat. You can use either the auxilliary
    files for a single partition (if all sites to plot come from that partition)
    or the merged auxilliary files for the entire run, but the latter requires
    more I/O and memory and is recommended only for small runs. You should supply
    either the -runDirectory (and optionally the -partitionMapFile) argument or
    the -auxFilePrefix argument.

  • -genderMapFile <map-file> : Path to a map file specifying the gender of
    each sample (optional). If supplied, the gender of each sample is shown for
    sites on chrX and chrY by overlaying the sample with a colored dot (blue for
    boys, red for girls). The map file should contain two tab-delimited columns,
    SAMPLE and GENDER (M/F).

3. Outputs

  • -O <output-file> : The destination output file (PDF) (required).

4. Running

java -Xmx2g -cp SVToolkit.jar:GenomeAnalysisTK.jar \ \ 
    -site DEL_P0001_1 \ 
    -site my_site_file.list \ 
    -O my_output_file.pdf \ 
    -runDirectory genotyping_run_dir
Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

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