PlotGenotypingResults documentation

PlotGenotypingResults

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.

Example

 java -Xmx4g -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

PlotGenotypingResults specific arguments

Name	Type	Default value	Summary
Required Outputs
-O	File	NA	Output file
Required Parameters
-site	List[String]	NA	Site ID or multiple site IDs .list file of sites to plot
Optional Inputs
-vcf	File	NA	Input sites file (vcf)
Optional Outputs
-log	String	NA	Set the logging location
Optional Parameters
-debug	String	NA	Enable verbose debugging output from R script
-genderMapFile	File	NA	Map file containing the gender for each sample
-l	String	INFO	Set the minimum level of logging
-outputFileFormat	String	PDF	Output file format (PDF or PNG)
-runDirectory	File	NA	Run directory used for the genotyping run
-sample	List[String]	NA	Sample(s) or .list file(s) of sample names
-truthDataFile	File	NA	File containing genotype truth data for some or all sites
-verbose	String	NA	Enable verbose output from R script
Optional Flags
-h	Flag	NA	Generate the help message
-version	Flag	NA	Output version information
Advanced Parameters
-auxFilePrefix	String	NA	Path prefix to auxilliary data files generated by genotyping (should be used only for small, non-partitioned runs)
-partitionMapFile	File	NA	Partition map file (defaults if runDirectory is supplied)
-plottingScript	String	NA	Custom plotting script to use (instead of default script)
-pretty	String	NA	Make prettier plots with less technical detail (default false)

Argument details

--auxFilePrefix / -auxFilePrefix ( String )

Path prefix to auxilliary data files generated by genotyping (should be used only for small, non-partitioned runs).

--debug / -debug ( String )

Enable verbose debugging output from R script.

--genderMapFile / -genderMapFile ( File )

Map file containing the gender for each sample.

--help / -h ( Flag )

Generate the help message.

--log_to_file / -log ( String )

Set the logging location.

--logging_level / -l ( String with default value INFO )

Set the minimum level of logging.

--outputFile / -O ( required File )

Output file.

--outputFileFormat / -outputFileFormat ( String with default value PDF )

Output file format (PDF or PNG).

--partitionMapFile / -partitionMapFile ( File )

Partition map file (defaults if runDirectory is supplied).

--plottingScript / -plottingScript ( String )

Custom plotting script to use (instead of default script).

--pretty / -pretty ( String )

Make prettier plots with less technical detail (default false).

--runDirectory / -runDirectory ( File )

Run directory used for the genotyping run.

Although this argument is technically optional, you need to provide it in almost all situations.

--sample / -sample ( List[String] )

Sample(s) or .list file(s) of sample names.

--site / -site ( required List[String] )

Site ID or multiple site IDs .list file of sites to plot.

--truthDataFile / -truthDataFile ( File )

File containing genotype truth data for some or all sites.

--vcfFile / -vcf ( File )

Input sites file (vcf).

--verbose / -verbose ( String )

Enable verbose output from R script.

--version / -version ( Flag )

Output version information.

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