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don't allow users to input priors anymore; they should be using heterozygosity and having the SSG calculate priors. 

Note that nothing was changed for dnSNP/hapmap priors (not sure what we want to do with these yet - any thoughts?)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1342 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-07-30 19:10:33 +00:00
parent b282635b05
commit fbc7d44bc7
1 changed files with 10 additions and 2 deletions
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12
java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
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@ -40,7 +40,7 @@ public class SingleSampleGenotyper extends LocusWalker<org.broadinstitute.sting.
@Argument(fullName = "call_indels", shortName = "indels", doc = "Call indels as well as point mutations", required = false) public Boolean CALL_INDELS = false;
// Control how the genotype hypotheses are weighed
@Argument(fullName = "priors_locus", shortName = "plocus", doc = "Comma-separated prior likelihoods for any locus (homref,het,homvar)", required = false) public String PRIORS_ANY_LOCUS = "0.999,0.000333,0.000667";
@Argument(fullName = "heterozygosity", shortName = "hets", doc = "Heterozygosity value used to compute prior likelihoods for any locus", required = false) public Double heterozygosity = 0.001;
@Argument(fullName = "priors_hapmap", shortName = "phapmap", doc = "Comma-separated prior likelihoods for Hapmap loci (homref,het,homvar)", required = false) public String PRIORS_HAPMAP = "0.999,1e-3,1e-5";
@Argument(fullName = "priors_dbsnp", shortName = "pdbsnp", doc = "Comma-separated prior likelihoods for dbSNP loci (homref,het,homvar)", required = false) public String PRIORS_DBSNP = "0.999,1e-3,1e-5";
@Argument(fullName = "priors_2nd_on", shortName = "p2ndon", doc = "Comma-separated prior likelihoods for the secondary bases of primary on-genotype bases (AA,AC,AG,AT,CC,CG,CT,GG,GT,TT)", required = false) public String PRIORS_2ND_ON = "0.000,0.302,0.366,0.142,0.000,0.548,0.370,0.000,0.319,0.000";
@ -103,11 +103,19 @@ public class SingleSampleGenotyper extends LocusWalker<org.broadinstitute.sting.
return pdbls;
}
private double[] computePriors(double h) {
double[] pdbls = new double[3];
pdbls[0] = 1.0 - (3.0 * h / 2.0);
pdbls[1] = h;
pdbls[2] = h / 2.0;
return pdbls;
}
/** Initialize the walker with some sensible defaults */
public void initialize() {
metricsOut = new AlleleMetrics(METRICS_FILE, LOD_THRESHOLD);
plocus = priorsArray(PRIORS_ANY_LOCUS);
plocus = computePriors(heterozygosity);
phapmap = priorsArray(PRIORS_HAPMAP);
pdbsnp = priorsArray(PRIORS_DBSNP);
p2ndon = priorsArray(PRIORS_2ND_ON);