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Revision as of 10:15, 29 October 2014
, 10:15, 29 October 2014→Hard Filtering Options
| colspan="3" | total number of samples between min & max, use logscale
| colspan="3" | total number of samples between min & max, use logscale
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| colspan="3" |
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{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! colspan="6" | Filters
|-
! Filter !! Configuration Key !! VCF value checked !! Filter Variants with... !! Default Value !! Conf Value Requirements
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| max Allele Balance in Heterozygotes || FILTER_MAX_ABL || INFO:AB || > ''conf value''/100.0 || 70,65 || < 100
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| max Strand Bias Pearson's Correlation || FILTER_MAX_STR || rowspan="2" | INFO:STR || > ''conf value''/100.0|| 20, 10 || < 100
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| min Strand Bias Pearson's Correlation || FILTER_MIN_STR || < ''conf value''/100.0 || -20, -10 || > -100
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| distance from known indel || FILTER_WIN_INDEL || position || distance from known indel < ''conf value'' || 5 || > 0
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| max Strand Bias z-score || FILTER_MAX_STZ || rowspan="2" | INFO:STZ || > ''conf value'' || 5, 10 || < INT_MAX
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| min Strand Bias z-score || FILTER_MIN_STZ || < ''conf value'' || -5, -10 || > INT_MIN
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| max Alternate allele inflation score || FILTER_MAX_AOI || INFO:AOI || > ''conf value'' || 5 || < INT_MAX
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| min FIC || FILTER_MIN_FIC || INFO:FIC || < ''conf value''/100.0 || -20, -10 || > INT_MIN
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| max Cycle Bias Peason's correlation || FILTER_MAX_CBR || INFO:CBR || > ''conf value''/100.0 || 20, 10 || < 100
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| max LQR || FILTER_MAX_LQR || INFO:LQR || > ''conf value''/100.0 || 30, 20 || < 100
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| min pred-scaled quality score || FILTER_MIN_QUAL || QUAL || < ''conf value'' || 5 || > 0
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| min Root Mean Squared Mapping Quality || FILTER_MIN_MQ || INFO:MQ || < ''conf value'' || 20 || > 0
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| max Fraction of bases with mapQ=0 || FILTER_MAX_MQ0 || INFO:MQ0 || > ''conf value''/100.0 || 10 || < 100
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| max Alternate allele quality z-score || FILTER_MAX_AOZ || INFO:AOZ || > ''conf value'' || || < INT_MAX
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| max Ratio of base-quality inflation || FILTER_MAX_IOR || INFO:IOR || > ''conf value'' || || < INT_MAX
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