umcg.genetica.io.pileup

Class PileupToVcf

java.lang.Object

umcg.genetica.io.pileup.PileupToVcf

public class PileupToVcf
extends Object

Author:

Patrick Deelen

Constructor Summary

Constructors

Constructor and Description
PileupToVcf()

Method Summary

Modifier and Type	Method and Description
static void	convertPileupToVcf(PileupFile pileupFile, String sample, File outputVcf, RandomAccessGenotypeData referenceGenotypes, int minBaseQuality) Parse pileup file and create vcf files with only SNPs that are in referenceGenotype data.
static void	convertPileupToVcf2(PileupFile pileupFile, String sample, File outputVcf, RandomAccessGenotypeData referenceGenotypes, int minBaseQuality) Parse pileup file and create vcf files with only SNPs that are in referenceGenotype data.
static void	main(String[] args)

Methods inherited from class java.lang.Object

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

Constructor Detail

PileupToVcf

public PileupToVcf()

Method Detail

main

public static void main(String[] args)
                 throws org.apache.commons.cli.ParseException,
                        IOException

Throws:

org.apache.commons.cli.ParseException

IOException

convertPileupToVcf

public static void convertPileupToVcf(PileupFile pileupFile,
                                      String sample,
                                      File outputVcf,
                                      RandomAccessGenotypeData referenceGenotypes,
                                      int minBaseQuality)
                               throws IOException

Parse pileup file and create vcf files with only SNPs that are in referenceGenotype data. VCF only contains the counts for the 2 alleles in the reference genotype data. Only parses the first samples in the pileup file

Parameters:

pileupFile -

sample -

outputVcf -

referenceGenotypes -

Throws:

IOException

convertPileupToVcf2

public static void convertPileupToVcf2(PileupFile pileupFile,
                                       String sample,
                                       File outputVcf,
                                       RandomAccessGenotypeData referenceGenotypes,
                                       int minBaseQuality)
                                throws IOException

Parse pileup file and create vcf files with only SNPs that are in referenceGenotype data. VCF only contains the counts for the 2 alleles in the reference genotype data. Only parses the first samples in the pileup file

Parameters:

pileupFile -

sample -

outputVcf -

referenceGenotypes -

Throws:

IOException