SetLowDepthGenosToMissingPlugin

This plugin sets genotypes to missing that have less than the user-specified minimum read depth. The genotypes must be from a source that provides read depth (for example, being read in from a VCF file will work, but not reading from a HapMap file). This plugin does not change the read depths.

The parameters to this plugin are:

• -minDepth <Integer>: minimum read depth below which genotypes are set to missing (restricted to the range 2 through 127).

Notice in the command line example below that a file is read into TASSEL before SetLowDepthGenosToMissingPlugin is called and that a file is written out after this plugin. SetLowDepthGenosToMissingPlugin itself does not directly read or write files. It simply handles genotypes in the middle. All depth information is kept, despite any changes in genotypes.

Example command line use:

#!code

 ./run_pipeline.pl -vcf myAppropriatelyNamed.vcf -SetLowDepthGenosToMissingPlugin -minDepth 7 -endPlugin -export myAppropriatelyNamedMinDepth7 -exportType VCF 

As you may notice, the file is read in before calling SetLowDepthGenosToMissingPlugin and the file is written out after the plugin. SetLowDepthGenosToMissingPlugin itself does not read or write files. It simply does what

Example use within a program:

#!java

GenotypeTable inputGenos = ImportUtils.read("myAppropriatelyNamed.vcf");

GenotypeTable outputGenos = new SetLowDepthGenosToMissingPlugin()
                                    .minDepth(7)
                                    .runPlugin(inputGenos);

writeToVCF(outputGenos, "myAppropriatelyNamedMinDepth7.vcf", true); // true for keepDepth