Merge pull request #1057 from broadinstitute/ldg_CGPvcfVerDoc

Clarify VCF version for supporting population alleles files

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmission.java

@@ -118,7 +118,9 @@ import java.util.*;
  *         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
  *         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>
  *
  * <h3>Output</h3>

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriors.java

@@ -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
-     * 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)
     public List<RodBinding<VariantContext>> supportVariants = new ArrayList<>();