Mercurial > repos > jjohnson > gatk2
comparison base_recalibrator.xml @ 23:2f9bf8bf42b7 draft
Replace covariate DinucCovariate with ContextCovariate
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 28 Dec 2012 12:34:05 -0600 |
| parents | bc18c5ad280f |
| children | 6460f2ba6a60 |
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| 22:bc18c5ad280f | 23:2f9bf8bf42b7 |
|---|---|
| 171 <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" help="-cov,--covariate &lt;covariate&gt;" > | 171 <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" help="-cov,--covariate &lt;covariate&gt;" > |
| 172 <!-- might we want to load the available covariates from an external configuration file, since additional ones can be added to local installs? --> | 172 <!-- might we want to load the available covariates from an external configuration file, since additional ones can be added to local installs? --> |
| 173 <option value="ReadGroupCovariate" /> | 173 <option value="ReadGroupCovariate" /> |
| 174 <option value="QualityScoreCovariate" /> | 174 <option value="QualityScoreCovariate" /> |
| 175 <option value="CycleCovariate" /> | 175 <option value="CycleCovariate" /> |
| 176 <option value="DinucCovariate" /> | 176 <option value="ContextCovariate" /> |
| 177 <!-- covariates below were pulled from list option --> | 177 <!-- covariates below were pulled from list option --> |
| 178 <option value="HomopolymerCovariate" /> | 178 <option value="HomopolymerCovariate" /> |
| 179 <option value="GCContentCovariate" /> | 179 <option value="GCContentCovariate" /> |
| 180 <option value="MappingQualityCovariate" /> | 180 <option value="MappingQualityCovariate" /> |
| 181 <option value="MinimumNQSCovariate" /> | 181 <option value="MinimumNQSCovariate" /> |