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- All Implemented Interfaces:
public class ComputeMedianGVCFAndFilter
TODO Separate Filter from FastaExtraction Created by zrm22 on 7/18/17. This class will filter a GVCF file based on user specified criteria and will export both the filtered GVCF and the fasta setquence that the DB loader expects. The user can provide the specified criteria using a config file(similar to db configs and the class will filter. Alternatively, the user can provide an upper and lower bound for poisson-based depth filtering. The following options are currently valid for filtering: exclusionString = String used for bcftools filtering. If this is specified, no additional terms are added to exclude DP_poisson_min = minimum poisson bound used for filtering(absolute minimum is 0.0) DP_poisson_max = maximum poisson bound used for filtering(absolute maximum is 1.0) DP_min = minimum DP bound DP_max = maximum DP bound GQ_min = minimum GQ bound GQ_max = maximum GQ bound QUAL_min = base quality minimum bound QUAL_max = base quality maximum bound filterHets = true/false or t/f, if true will filter sites where 2 or more alleles have above 0 AD
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Method Summary
Modifier and Type Method Description static void
filterAndExtractFasta(Path gvcfFile, String outputDirectory, GenomeSequence refSeq, String intervalFile, Properties filterProperties, boolean isAssembly, String bcfToolsPath)
Method to filter the gvcf and extract the fasta using the config file. static void
filterAndExtractFasta(Path gvcfFile, String outputDirectory, GenomeSequence refSeq, String intervalFile, Tuple<Double, Double> poissonProbabliltyBounds, boolean isAssembly, String bcfToolsPath)
Old method using a poissonProbability tuple to filter based on depth. static String
filterGVCF(String inputFile, String outputFile, Properties configProperties, boolean isAssembly, String bcftools)
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Method Detail
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filterAndExtractFasta
static void filterAndExtractFasta(Path gvcfFile, String outputDirectory, GenomeSequence refSeq, String intervalFile, Properties filterProperties, boolean isAssembly, String bcfToolsPath)
Method to filter the gvcf and extract the fasta using the config file.
- Parameters:
gvcfFile
- GVCF file to be filteredoutputDirectory
- Directory to store the gvcfs and fastasrefSeq
- Reference genome sequenceintervalFile
- interval bed file holding the intervals we need to export for the fastasfilterProperties
- Properties object using the configisAssembly
- Boolean saying if the gvcf is an assembly or not.bcfToolsPath
- Path
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filterAndExtractFasta
static void filterAndExtractFasta(Path gvcfFile, String outputDirectory, GenomeSequence refSeq, String intervalFile, Tuple<Double, Double> poissonProbabliltyBounds, boolean isAssembly, String bcfToolsPath)
Old method using a poissonProbability tuple to filter based on depth. This should be deprecated once we tune the pipeline TODO deprecate this method once the pipeline is tuned.
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filterGVCF
static String filterGVCF(String inputFile, String outputFile, Properties configProperties, boolean isAssembly, String bcftools)
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