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Merge pull request #401 from broadinstitute/gg_vqsr_ignorefilter_doc 

Minor clarifications regarding ignoreFilter argument
This commit is contained in:
Ryan Poplin 2013-09-27 07:05:41 -07:00
parent a29f1f84bf 27808d336a
commit cba9668641
2 changed files with 8 additions and 2 deletions
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5
protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
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@ -136,7 +136,10 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
/////////////////////////////
@Argument(fullName="ts_filter_level", shortName="ts_filter_level", doc="The truth sensitivity level at which to start filtering", required=false)
protected double TS_FILTER_LEVEL = 99.0;
@Argument(fullName="ignore_filter", shortName="ignoreFilter", doc="If specified the variant recalibrator will use variants even if the specified filter name is marked in the input VCF file", required=false)
/**
* For this to work properly, the -ignoreFilter argument should also be applied to the VariantRecalibration command.
*/
@Argument(fullName="ignore_filter", shortName="ignoreFilter", doc="If specified, the recalibration will be applied to variants marked as filtered by the specified filter name in the input VCF file", required=false)
private String[] IGNORE_INPUT_FILTERS = null;
@Argument(fullName="excludeFiltered", shortName="ef", doc="Don't output filtered loci after applying the recalibration", required=false)
protected boolean EXCLUDE_FILTERED = false;

5
protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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@ -201,7 +201,10 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
*/
@Argument(fullName="TStranche", shortName="tranche", doc="The levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)", required=false)
private double[] TS_TRANCHES = new double[] {100.0, 99.9, 99.0, 90.0};
@Argument(fullName="ignore_filter", shortName="ignoreFilter", doc="If specified the variant recalibrator will use variants even if the specified filter name is marked in the input VCF file", required=false)
/**
* For this to work properly, the -ignoreFilter argument should also be applied to the ApplyRecalibration command.
*/
@Argument(fullName="ignore_filter", shortName="ignoreFilter", doc="If specified, the variant recalibrator will also use variants marked as filtered by the specified filter name in the input VCF file", required=false)
private String[] IGNORE_INPUT_FILTERS = null;
@Output(fullName="rscript_file", shortName="rscriptFile", doc="The output rscript file generated by the VQSR to aid in visualization of the input data and learned model", required=false, defaultToStdout=false)
private File RSCRIPT_FILE = null;