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Clarify VCF version for supporting population alleles files 

Clarify DeNovoPrior definition on PbyT
This commit is contained in:
Laura Gauthier 2015-07-20 13:22:40 -04:00
parent b296576505
commit 8c18ead5e4
2 changed files with 4 additions and 2 deletions
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4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmission.java
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@ -118,7 +118,9 @@ import java.util.*;
* remain in mendelian violation after being assigned the most likely genotype combination will be reported * remain in mendelian violation after being assigned the most likely genotype combination will be reported
* there. Information reported: chromosome, position, filter, allele count in VCF, family, transmission * there. Information reported: chromosome, position, filter, allele count in VCF, family, transmission
* probability, and each individual genotype, depth, allelic depth and likelihoods.</li> * probability, and each individual genotype, depth, allelic depth and likelihoods.</li>
* <li>DeNovoPrior: Mutation prio; default is 1e-8</li> * <li>DeNovoPrior: Prior probability of de novo mutations. The default value of 1e-8 is fairly stringent, so if
* you are interested in maximizing sensitivity at the expense of specificity (i.e. are ok with seeing some false
* positives as long as all true positives are detected) you will need to relax this value.</li>
* </ul> * </ul>
* *
* <h3>Output</h3> * <h3>Output</h3>

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriors.java
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@ -196,7 +196,7 @@ public class CalculateGenotypePosteriors extends RodWalker<Integer,Integer> {
/** /**
* Supporting external panels. Allele counts from these panels (taken from AC,AN or MLEAC,AN or raw genotypes) will * Supporting external panels. Allele counts from these panels (taken from AC,AN or MLEAC,AN or raw genotypes) will
* be used to inform the frequency distribution underying the genotype priors. * be used to inform the frequency distribution underying the genotype priors. These files must be VCF 4.2 spec or later.
*/ */
@Input(fullName="supporting", shortName = "supporting", doc="Other callsets to use in generating genotype posteriors", required=false) @Input(fullName="supporting", shortName = "supporting", doc="Other callsets to use in generating genotype posteriors", required=false)
public List<RodBinding<VariantContext>> supportVariants = new ArrayList<>(); public List<RodBinding<VariantContext>> supportVariants = new ArrayList<>();