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Another fix to VQSR docs

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Ryan Poplin 2012-08-01 14:52:49 -04:00
parent 4093909a56
commit fabca66d09
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public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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@ -63,7 +63,7 @@ import java.util.*;
* The purpose of the variant recalibrator is to assign a well-calibrated probability to each variant call in a call set.
* One can then create highly accurate call sets by filtering based on this single estimate for the accuracy of each call.
* The approach taken by variant quality score recalibration is to develop a continuous, covarying estimate of the relationship
* between SNP call annotations (QD, SB, HaplotypeScore, HRun, for example) and the the probability that a SNP is a true genetic
* between SNP call annotations (QD, MQ, HaplotypeScore, and ReadPosRankSum, for example) and the the probability that a SNP is a true genetic
* variant versus a sequencing or data processing artifact. This model is determined adaptively based on "true sites" provided
* as input, typically HapMap 3 sites and those sites found to be polymorphic on the Omni 2.5M SNP chip array. This adaptive
* error model can then be applied to both known and novel variation discovered in the call set of interest to evaluate the