From d241f0e9031882a65b71d421cd2624513d0f46ba Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 1 Sep 2011 21:57:02 -0400 Subject: [PATCH] Adding docs for the pcr error rate argument. --- .../gatk/walkers/genotyper/UnifiedArgumentCollection.java | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index ae419a5c4..7b8045581 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -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;