PlotGenotypingResults

Geraldine_VdAuwera

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 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 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 \
    org.broadinstitute.sv.apps.PlotGenotypingResults \ 
    -site DEL_P0001_1 \ 
    -site my_site_file.list \ 
    -O my_output_file.pdf \ 
    -runDirectory genotyping_run_dir