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Update to the VSS GATK documentation.

This commit is contained in:
Christopher Hartl 2012-01-03 13:39:31 -05:00
parent 4984ca5e31
commit 93e1417b6e
1 changed files with 37 additions and 9 deletions
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46
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelectorWalker.java
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@ -106,37 +106,70 @@ public class ValidationSiteSelectorWalker extends RodWalker<Integer, Integer> {
POLY_BASED_ON_GL
}
/**
* The input VCF file
*/
@Input(fullName="variant", shortName = "V", doc="Input VCF file, can be specified multiple times", required=true)
public List<RodBinding<VariantContext>> variants;
/**
* The output VCF file
*/
@Output(doc="File to which variants should be written",required=true)
protected VCFWriter vcfWriter = null;
/**
* Sample name(s) to subset the input VCF to, prior to selecting variants. -sn A -sn B subsets to samples A and B.
*/
@Argument(fullName="sample_name", shortName="sn", doc="Include genotypes from this sample. Can be specified multiple times", required=false)
public Set<String> sampleNames = new HashSet<String>(0);
/**
* Sample regexps to subset the input VCF to, prior to selecting variants. -sn NA12* subsets to all samples with prefix NA12
*/
@Argument(fullName="sample_expressions", shortName="se", doc="Regular expression to select many samples from the ROD tracks provided. Can be specified multiple times", required=false)
public Set<String> sampleExpressions ;
/**
* File containing a list of sample names to subset the input vcf to. Equivalent to specifying the contents of the file separately with -sn
*/
@Input(fullName="sample_file", shortName="sf", doc="File containing a list of samples (one per line) to include. Can be specified multiple times", required=false)
public Set<File> sampleFiles;
/**
* A mode for selecting sites based on sample-level data. See the wiki documentation for more information.
*/
@Argument(fullName="sampleMode", shortName="sampleMode", doc="Sample selection mode", required=false)
private SAMPLE_SELECTION_MODE sampleMode = SAMPLE_SELECTION_MODE.NONE;
/**
* An P[nonref] threshold for SAMPLE_SELECTION_MODE=POLY_BASED_ON_GL. See the wiki documentation for more information.
*/
@Argument(shortName="samplePNonref",fullName="samplePNonref", doc="GL-based selection mode only: the probability" +
" that a site is non-reference in the samples for which to include the site",required=false)
private double samplePNonref = 0.99;
/**
* The number of sites in your validation set
*/
@Argument(fullName="numValidationSites", shortName="numSites", doc="Number of output validation sites", required=true)
private int numValidationSites;
/**
* Do not exclude filtered sites (e.g. not PASS or .) from consideration for validation
*/
@Argument(fullName="includeFilteredSites", shortName="ifs", doc="If true, will include filtered sites in set to choose variants from", required=false)
private boolean INCLUDE_FILTERED_SITES = false;
/**
* Argument for the frequency selection mode. (AC/AF/AN) are taken from VCF info field, not recalculated. Typically specified for sites-only VCFs that still have AC/AF/AN information.
*/
@Argument(fullName="ignoreGenotypes", shortName="ignoreGenotypes", doc="If true, will ignore genotypes in VCF, will take AC,AF from annotations and will make no sample selection", required=false)
private boolean IGNORE_GENOTYPES = false;
/**
* Argument for the frequency selection mode. Allows reference (non-polymorphic) sites to be included in the validation set.
*/
@Argument(fullName="ignorePolymorphicStatus", shortName="ignorePolymorphicStatus", doc="If true, will ignore polymorphic status in VCF, and will take VCF record directly without pre-selection", required=false)
private boolean IGNORE_POLYMORPHIC = false;
@ -145,19 +178,14 @@ public class ValidationSiteSelectorWalker extends RodWalker<Integer, Integer> {
private int numFrequencyBins = 20;
/**
* This argument selects allele frequency selection mode:
* KEEP_AF_SPECTRUM will choose variants so that the resulting allele frequency spectrum matches as closely as possible the input set
* UNIFORM will choose variants uniformly without regard to their allele frequency.
*
*/
* This argument selects allele frequency selection mode. See the wiki for more information.
*/
@Argument(fullName="frequencySelectionMode", shortName="freqMode", doc="Allele Frequency selection mode", required=false)
private AF_COMPUTATION_MODE freqMode = AF_COMPUTATION_MODE.KEEP_AF_SPECTRUM;
/**
* This argument selects particular kinds of variants out of a list. If left empty, there is no type selection and all variant types are considered for other selection criteria.
* When specified one or more times, a particular type of variant is selected.
*
*/
* This argument selects particular kinds of variants (i.e. SNP, INDEL) out of a list. If left unspecified, all types are considered.
*/
@Argument(fullName="selectTypeToInclude", shortName="selectType", doc="Select only a certain type of variants from the input file. Valid types are INDEL, SNP, MIXED, MNP, SYMBOLIC, NO_VARIATION. Can be specified multiple times", required=false)
private List<VariantContext.Type> TYPES_TO_INCLUDE = new ArrayList<VariantContext.Type>();