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Better docs on the meaning of heterozygosity 

-- [delivers #53522209]
This commit is contained in:
Mark DePristo 2013-07-24 08:44:51 -04:00
parent dd0e6409c6
commit 318f7e74e4
1 changed files with 28 additions and 4 deletions
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32
protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
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@ -68,16 +68,40 @@ import java.util.Map;
public class StandardCallerArgumentCollection { public class StandardCallerArgumentCollection {
/** /**
* The expected heterozygosity value used to compute prior likelihoods for any locus. The default priors are: * The expected heterozygosity value used to compute prior probability that a locus is non-reference.
* het = 1e-3, P(hom-ref genotype) = 1 - 3 * het / 2, P(het genotype) = het, P(hom-var genotype) = het / 2 *
* The default priors are for provided for humans:
*
* het = 1e-3
*
* which means that the probability of N samples being hom-ref at a site is:
*
* 1 - sum_i_2N (het / i)
*
* Note that heterozygosity as used here is the population genetics concept:
*
* http://en.wikipedia.org/wiki/Zygosity#Heterozygosity_in_population_genetics
*
* That is, a hets value of 0.01 implies that two randomly chosen chromosomes from the population of organisms
* would differ from each other (one being A and the other B) at a rate of 1 in 100 bp.
*
* Note that this quantity has nothing to do with the likelihood of any given sample having a heterozygous genotype,
* which in the GATK is purely determined by the probability of the observed data P(D | AB) under the model that there
* may be a AB het genotype. The posterior probability of this AB genotype would use the het prior, but the GATK
* only uses this posterior probability in determining the prob. that a site is polymorphic. So changing the
* het parameters only increases the chance that a site will be called non-reference across all samples, but
* doesn't actually change the output genotype likelihoods at all, as these aren't posterior probabilities at all.
*
* The quantity that changes whether the GATK considers the possibility of a het genotype at all is the ploidy,
* which determines how many chromosomes each individual in the species carries.
*/ */
@Argument(fullName = "heterozygosity", shortName = "hets", doc = "Heterozygosity value used to compute prior likelihoods for any locus", required = false) @Argument(fullName = "heterozygosity", shortName = "hets", doc = "Heterozygosity value used to compute prior likelihoods for any locus. See the GATKDocs for full details on the meaning of this population genetics concept", required = false)
public Double heterozygosity = UnifiedGenotyperEngine.HUMAN_SNP_HETEROZYGOSITY; public Double heterozygosity = UnifiedGenotyperEngine.HUMAN_SNP_HETEROZYGOSITY;
/** /**
* This argument informs the prior probability of having an indel at a site. * This argument informs the prior probability of having an indel at a site.
*/ */
@Argument(fullName = "indel_heterozygosity", shortName = "indelHeterozygosity", doc = "Heterozygosity for indel calling", required = false) @Argument(fullName = "indel_heterozygosity", shortName = "indelHeterozygosity", doc = "Heterozygosity for indel calling. See the GATKDocs for heterozygosity for full details on the meaning of this population genetics concept", required = false)
public double INDEL_HETEROZYGOSITY = 1.0/8000; public double INDEL_HETEROZYGOSITY = 1.0/8000;
@Argument(fullName = "genotyping_mode", shortName = "gt_mode", doc = "Specifies how to determine the alternate alleles to use for genotyping", required = false) @Argument(fullName = "genotyping_mode", shortName = "gt_mode", doc = "Specifies how to determine the alternate alleles to use for genotyping", required = false)