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Adding docs for the pcr error rate argument.

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Eric Banks 2011-09-01 21:57:02 -04:00
parent ad4ea0b80b
commit d241f0e903
1 changed files with 5 additions and 0 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -52,6 +52,11 @@ public class UnifiedArgumentCollection {
@Argument(fullName = "heterozygosity", shortName = "hets", doc = "Heterozygosity value used to compute prior likelihoods for any locus", required = false)
public Double heterozygosity = DiploidSNPGenotypePriors.HUMAN_HETEROZYGOSITY;
/**
* The PCR error rate is independent of the sequencing error rate, which is necessary because we cannot necessarily
* distinguish between PCR errors vs. sequencing errors. The practical implication for this value is that it
* effectively acts as a cap on the base qualities.
*/
@Argument(fullName = "pcr_error_rate", shortName = "pcr_error", doc = "The PCR error rate to be used for computing fragment-based likelihoods", required = false)
public Double PCR_error = DiploidSNPGenotypeLikelihoods.DEFAULT_PCR_ERROR_RATE;