Package picard.vcf.filter
Class AlleleBalanceFilter
java.lang.Object
picard.vcf.filter.AlleleBalanceFilter
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VariantFilter
Filters out a record if the allele balance for heterozygotes is out of a defined range across all samples.
The threshold is set as the minimum fraction of the data drawn from the less-represented allele - e.g. 0.3 would
set that whichever allele has lower representation across all heterozygous individuals must account for at least 30% of the
total observations.
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Field Summary
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Constructor Summary
Constructors -
Method Summary
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Field Details
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AB_FILTER
The filter string used for sites that fail the allele balance filter.- See Also:
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Constructor Details
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AlleleBalanceFilter
public AlleleBalanceFilter(double hetAlleleBalance)
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Method Details
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headerLines
Description copied from interface:VariantFilter
Return VCF header lines that define filters that may be applied by the VariantFilter.- Specified by:
headerLines
in interfaceVariantFilter
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filter
Description copied from interface:VariantFilter
Check to see if the VariantContext should have a filter applied to it. If so return the filter string, otherwise return null.- Specified by:
filter
in interfaceVariantFilter
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