Mercurial > repos > jjohnson > gatk2
comparison unified_genotyper.xml @ 37:dd9f8ea2b718 draft
unified_genotyper - indelGap penalty param need to be integer values
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 01 Mar 2013 12:43:41 -0600 |
| parents | 14d47237bb0a |
| children | 1061731ba6ed |
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| 36:14d47237bb0a | 37:dd9f8ea2b718 |
|---|---|
| 469 <param name="min_base_quality_score" type="integer" value="17" label="Minimum base quality required to consider a base for calling" help="-mbq,--min_base_quality_score &lt;min_base_quality_score&gt;" /> | 469 <param name="min_base_quality_score" type="integer" value="17" label="Minimum base quality required to consider a base for calling" help="-mbq,--min_base_quality_score &lt;min_base_quality_score&gt;" /> |
| 470 <param name="max_deletion_fraction" type="float" value="0.05" label="Maximum fraction of reads with deletions spanning this locus for it to be callable" help="to disable, set to < 0 or > 1 (-deletions,--max_deletion_fraction &lt;max_deletion_fraction&gt;)" /> | 470 <param name="max_deletion_fraction" type="float" value="0.05" label="Maximum fraction of reads with deletions spanning this locus for it to be callable" help="to disable, set to < 0 or > 1 (-deletions,--max_deletion_fraction &lt;max_deletion_fraction&gt;)" /> |
| 471 <param name="max_alternate_alleles" type="integer" value="6" label="Maximum number of alternate alleles to genotype" help="-maxAlleles,--max_alternate_alleles &lt;max_alternate_alleles&gt;" /> | 471 <param name="max_alternate_alleles" type="integer" value="6" label="Maximum number of alternate alleles to genotype" help="-maxAlleles,--max_alternate_alleles &lt;max_alternate_alleles&gt;" /> |
| 472 <param name="min_indel_count_for_genotyping" type="integer" value="5" label="Minimum number of consensus indels required to trigger genotyping run" help="-minIndelCnt,--min_indel_count_for_genotyping &lt;min_indel_count_for_genotyping&gt;" /> | 472 <param name="min_indel_count_for_genotyping" type="integer" value="5" label="Minimum number of consensus indels required to trigger genotyping run" help="-minIndelCnt,--min_indel_count_for_genotyping &lt;min_indel_count_for_genotyping&gt;" /> |
| 473 <param name="indel_heterozygosity" type="float" value="0.000125" label="Heterozygosity for indel calling" help="1.0/8000==0.000125 (-indelHeterozygosity,--indel_heterozygosity &lt;indel_heterozygosity&gt;)"/> | 473 <param name="indel_heterozygosity" type="float" value="0.000125" label="Heterozygosity for indel calling" help="1.0/8000==0.000125 (-indelHeterozygosity,--indel_heterozygosity &lt;indel_heterozygosity&gt;)"/> |
| 474 <param name="indelGapContinuationPenalty" type="float" value="10.0" label="Indel gap continuation penalty" help="--indelGapContinuationPenalty" /> | 474 <param name="indelGapContinuationPenalty" type="integer" value="10" label="Indel gap continuation penalty" help="--indelGapContinuationPenalty"> |
| 475 <param name="indelGapOpenPenalty" type="float" value="45.0" label="Indel gap open penalty" help="--indelGapOpenPenalty" /> | 475 <help>Indel gap continuation penalty, as Phred-scaled probability. I.e., 30 => 10^-30/10.</help> |
| 476 <validator type="in_range" message="value between 0 and 255" min="0" max="255"/> | |
| 477 </param> | |
| 478 <param name="indelGapOpenPenalty" type="integer" value="45" label="Indel gap open penalty" help="--indelGapOpenPenalty" > | |
| 479 <help>Indel gap open penalty, as Phred-scaled probability. I.e., 30 => 10^-30/10.</help> | |
| 480 <validator type="in_range" message="value between 0 and 255" min="0" max="255"/> | |
| 481 </param> | |
| 482 <!-- indelHaplotypeSize - Gone in GATK 2.4? --> | |
| 476 <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" help="--indelHaplotypeSize" /> | 483 <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" help="--indelHaplotypeSize" /> |
| 477 <param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" help="--doContextDependentGapPenalties" /> | 484 <param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" help="--doContextDependentGapPenalties" /> |
| 478 <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation &lt;annotation&gt;"> | 485 <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation &lt;annotation&gt;"> |
| 479 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> | 486 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> |
| 480 <options from_data_table="gatk2_annotations"> | 487 <options from_data_table="gatk2_annotations"> |