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Merge pull request #745 from broadinstitute/ldg_VariantAnnotatorDocs 

Added docs to VariantFiltration is accordance with new htsjdk changes.  ...
This commit is contained in:
ldgauthier 2014-10-10 14:11:24 -04:00
parent 22a3c6e556 0ecb85d321
commit d259f3c84f
2 changed files with 3 additions and 2 deletions
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2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java
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@ -135,7 +135,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
protected VariantContextWriter vcfWriter = null;
/**
* See the -list argument to view available annotations.
* See the --list argument to view available annotations.
*/
@Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls", required=false)
protected List<String> annotationsToUse = new ArrayList<>();

3
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java
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@ -115,7 +115,8 @@ public class VariantFiltration extends RodWalker<Integer, Integer> {
* Similar to the INFO field based expressions, but used on the FORMAT (genotype) fields instead.
* VariantFiltration will add the sample-level FT tag to the FORMAT field of filtered samples (this does not affect the record's FILTER tag).
* One can filter normally based on most fields (e.g. "GQ < 5.0"), but the GT (genotype) field is an exception. We have put in convenience
* methods so that one can now filter out hets ("isHet == 1"), refs ("isHomRef == 1"), or homs ("isHomVar == 1").
* methods so that one can now filter out hets ("isHet == 1"), refs ("isHomRef == 1"), or homs ("isHomVar == 1"). Also available are
* expressions isCalled, isNoCall, isMixed, and isAvailable, in accordance with the methods of the Genotype object.
*/
@Argument(fullName="genotypeFilterExpression", shortName="G_filter", doc="One or more expression used with FORMAT (sample/genotype-level) fields to filter (see documentation guide for more info)", required=false)
protected ArrayList<String> GENOTYPE_FILTER_EXPS = new ArrayList<String>();