public class PileupToVcf extends Object
| Constructor and Description |
|---|
PileupToVcf() |
| 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) |
public static void main(String[] args) throws org.apache.commons.cli.ParseException, IOException
org.apache.commons.cli.ParseExceptionIOExceptionpublic static void convertPileupToVcf(PileupFile pileupFile, String sample, File outputVcf, RandomAccessGenotypeData referenceGenotypes, int minBaseQuality) throws IOException
pileupFile - sample - outputVcf - referenceGenotypes - IOExceptionpublic static void convertPileupToVcf2(PileupFile pileupFile, String sample, File outputVcf, RandomAccessGenotypeData referenceGenotypes, int minBaseQuality) throws IOException
pileupFile - sample - outputVcf - referenceGenotypes - IOExceptionCopyright © 2015. All Rights Reserved.