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Updated docs to tell users not to use PCR indel error modeling for PCR free data.

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Eric Banks 2013-09-23 15:48:47 -04:00
parent 5bbad75402
commit d6992d1263
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protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -475,6 +475,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
/** /**
* Which PCR indel error model should we use when calculating likelihoods? If NONE is selected, then the default base * Which PCR indel error model should we use when calculating likelihoods? If NONE is selected, then the default base
* insertion/deletion qualities will be used (or taken from the read if generated through the BaseRecalibrator). * insertion/deletion qualities will be used (or taken from the read if generated through the BaseRecalibrator).
* VERY IMPORTANT: when using PCR-free sequencing data we definitely recommend setting this argument to NONE.
*/ */
@Advanced @Advanced
@Argument(fullName = "pcr_indel_model", shortName = "pcrModel", doc = "The PCR indel model to use", required = false) @Argument(fullName = "pcr_indel_model", shortName = "pcrModel", doc = "The PCR indel model to use", required = false)