Mercurial > repos > jjohnson > gatk2
changeset 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 |
| files | unified_genotyper.xml |
| diffstat | 1 files changed, 9 insertions(+), 2 deletions(-) [+] |
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--- a/unified_genotyper.xml Fri Mar 01 08:07:56 2013 -0600 +++ b/unified_genotyper.xml Fri Mar 01 12:43:41 2013 -0600 @@ -471,8 +471,15 @@ <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;" /> <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;" /> <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;)"/> - <param name="indelGapContinuationPenalty" type="float" value="10.0" label="Indel gap continuation penalty" help="--indelGapContinuationPenalty" /> - <param name="indelGapOpenPenalty" type="float" value="45.0" label="Indel gap open penalty" help="--indelGapOpenPenalty" /> + <param name="indelGapContinuationPenalty" type="integer" value="10" label="Indel gap continuation penalty" help="--indelGapContinuationPenalty"> + <help>Indel gap continuation penalty, as Phred-scaled probability. I.e., 30 => 10^-30/10.</help> + <validator type="in_range" message="value between 0 and 255" min="0" max="255"/> + </param> + <param name="indelGapOpenPenalty" type="integer" value="45" label="Indel gap open penalty" help="--indelGapOpenPenalty" > + <help>Indel gap open penalty, as Phred-scaled probability. I.e., 30 => 10^-30/10.</help> + <validator type="in_range" message="value between 0 and 255" min="0" max="255"/> + </param> + <!-- indelHaplotypeSize - Gone in GATK 2.4? --> <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" help="--indelHaplotypeSize" /> <param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" help="--doContextDependentGapPenalties" /> <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation &lt;annotation&gt;">