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Change the HC's phredScaledGlobalReadMismappingRate from 60 to 45, because Ryan and Mark told me to.

This commit is contained in:
Eric Banks 2013-06-03 14:34:29 -04:00
parent 77868d034f
commit c0e3874db0
1 changed files with 1 additions and 1 deletions
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protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -336,7 +336,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
*/ */
@Advanced @Advanced
@Argument(fullName="phredScaledGlobalReadMismappingRate", shortName="globalMAPQ", doc="The global assumed mismapping rate for reads", required = false) @Argument(fullName="phredScaledGlobalReadMismappingRate", shortName="globalMAPQ", doc="The global assumed mismapping rate for reads", required = false)
protected int phredScaledGlobalReadMismappingRate = 60; protected int phredScaledGlobalReadMismappingRate = 45;
@Advanced @Advanced
@Argument(fullName="maxNumHaplotypesInPopulation", shortName="maxNumHaplotypesInPopulation", doc="Maximum number of haplotypes to consider for your population. This number will probably need to be increased when calling organisms with high heterozygosity.", required = false) @Argument(fullName="maxNumHaplotypesInPopulation", shortName="maxNumHaplotypesInPopulation", doc="Maximum number of haplotypes to consider for your population. This number will probably need to be increased when calling organisms with high heterozygosity.", required = false)