net.maizegenetics.pangenome.gvcfFiltering

Class ComputeMedianGVCFAndFilter

java.lang.Object

net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianGVCFAndFilter

public class ComputeMedianGVCFAndFilter
extends Object

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

Constructor Summary

Constructors

Constructor and Description
ComputeMedianGVCFAndFilter()

Method Summary

Modifier and Type	Method and Description
static void	filterAndExtractFasta(Path gvcfFile, String outputDirectory, net.maizegenetics.dna.map.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, net.maizegenetics.dna.map.GenomeSequence refSeq, String intervalFile, net.maizegenetics.util.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)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ComputeMedianGVCFAndFilter

public ComputeMedianGVCFAndFilter()

Method Detail

filterAndExtractFasta

public static void filterAndExtractFasta(Path gvcfFile,
                                         String outputDirectory,
                                         net.maizegenetics.dna.map.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 filtered

outputDirectory - Directory to store the gvcfs and fastas

refSeq - Reference genome sequence

intervalFile - interval bed file holding the intervals we need to export for the fastas

filterProperties - Properties object using the config

isAssembly - Boolean saying if the gvcf is an assembly or not. If an assembly, we only exclude based on depth

bcfToolsPath - Path

filterAndExtractFasta

public static void filterAndExtractFasta(Path gvcfFile,
                                         String outputDirectory,
                                         net.maizegenetics.dna.map.GenomeSequence refSeq,
                                         String intervalFile,
                                         net.maizegenetics.util.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.

Parameters:

gvcfFile -

outputDirectory -

refSeq -

intervalFile -

poissonProbabliltyBounds -

isAssembly -

bcfToolsPath -

filterGVCF

public static String filterGVCF(String inputFile,
                                String outputFile,
                                Properties configProperties,
                                boolean isAssembly,
                                String bcftools)