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# PlotGenotypingResults

edited September 2012

### 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
genotype for each sample. This utility requires information from auxilliary
data files produced during genotyping which are written to the genotyping run
directory.

### 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 partition.genotypes.map.dat in the specified
run directory. If you did not use parallel genotyping, you need to supply

• -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 \