public class DiscoverySNPCallerPlugin
extends AbstractPlugin
This class aligns tags at the same physical location against one another, calls SNPs, and then outputs the SNPs to a HapMap file. It is multi-threaded, as there are substantial speed increases with it.
public DiscoverySNPCallerPlugin()
public DiscoverySNPCallerPlugin(java.awt.Frame parentFrame,
boolean isInteractive)
public void postProcessParameters()
public java.lang.String inputTagsByTaxaFile()
Input TagsByTaxa file (if hdf5 format, use .hdf or .h5 extension)
public DiscoverySNPCallerPlugin inputTagsByTaxaFile(java.lang.String value)
Set Input Tags by Taxa File. Input TagsByTaxa file (if hdf5 format, use .hdf or .h5 extension)
value - Input Tags by Taxa Filepublic java.lang.Boolean useByteFormat()
Use byte format TagsByTaxa file (*.tbt.byte)
public DiscoverySNPCallerPlugin useByteFormat(java.lang.Boolean value)
Set Use Byte Format. Use byte format TagsByTaxa file (*.tbt.byte)
value - Use Byte Formatpublic java.lang.String inputTOPMFile()
TagsOnPhysicalMap (TOPM) file containing genomic positions of tags
public DiscoverySNPCallerPlugin inputTOPMFile(java.lang.String value)
Set Input TOPM File. TagsOnPhysicalMap (TOPM) file containing genomic positions of tags
value - Input TOPM Filepublic java.lang.String outputTOPMFile()
Output TagsOnPhysicalMap (TOPM) file with allele calls (variants) added (for use with ProductionSNPCallerPlugin
public DiscoverySNPCallerPlugin outputTOPMFile(java.lang.String value)
Set Output TOPM File. Output TagsOnPhysicalMap (TOPM) file with allele calls (variants) added (for use with ProductionSNPCallerPlugin
value - Output TOPM Filepublic java.lang.String logFile()
TagLocus log file name
public DiscoverySNPCallerPlugin logFile(java.lang.String value)
Set Log File. TagLocus log file name
value - Log Filepublic java.lang.Double minimumF()
Minimum F (inbreeding coefficient)
public DiscoverySNPCallerPlugin minimumF(java.lang.Double value)
Set Minimum F. Minimum F (inbreeding coefficient)
value - Minimum Fpublic java.lang.String pedigreeFile()
Pedigree file containing full sample names (or expected names after merging) & expected inbreeding coefficient (F) for each. Only taxa with expected F >= mnF used to calculate F = 1-Ho/He. (default: use ALL taxa to calculate F
public DiscoverySNPCallerPlugin pedigreeFile(java.lang.String value)
Set Pedigree File. Pedigree file containing full sample names (or expected names after merging) & expected inbreeding coefficient (F) for each. Only taxa with expected F >= mnF used to calculate F = 1-Ho/He. (default: use ALL taxa to calculate F
value - Pedigree Filepublic java.lang.Double minMinorAlleleFreq()
Minimum minor allele frequency
public DiscoverySNPCallerPlugin minMinorAlleleFreq(java.lang.Double value)
Set Min Minor Allele Freq. Minimum minor allele frequency
value - Min Minor Allele Freqpublic java.lang.Integer minMinorAlleleCount()
Minimum minor allele count
public DiscoverySNPCallerPlugin minMinorAlleleCount(java.lang.Integer value)
Set Min Minor Allele Count. Minimum minor allele count
value - Min Minor Allele Countpublic java.lang.Double minLocusCoverage()
Minimum locus coverage (proportion of Taxa with a genotype)
public DiscoverySNPCallerPlugin minLocusCoverage(java.lang.Double value)
Set Min Locus Coverage. Minimum locus coverage (proportion of Taxa with a genotype)
value - Min Locus Coveragepublic java.lang.Double aveSeqErrorRate()
Average sequencing error rate per base (used to decide between heterozygous and homozygous calls)
public DiscoverySNPCallerPlugin aveSeqErrorRate(java.lang.Double value)
Set Ave Seq Error Rate. Average sequencing error rate per base (used to decide between heterozygous and homozygous calls)
value - Ave Seq Error Ratepublic java.lang.String referenceGenomeFile()
Path to reference genome in fasta format. Ensures that a tag from the reference genome is always included when the tags at a locus are aligned against each other to call SNPs. The reference allele for each site is then provided in the output HapMap files, under the taxon name "REFERENCE_GENOME" (first taxon). DEFAULT: Don't use reference genome.
public DiscoverySNPCallerPlugin referenceGenomeFile(java.lang.String value)
Set Reference Genome File. Path to reference genome in fasta format. Ensures that a tag from the reference genome is always included when the tags at a locus are aligned against each other to call SNPs. The reference allele for each site is then provided in the output HapMap files, under the taxon name "REFERENCE_GENOME" (first taxon). DEFAULT: Don't use reference genome.
value - Reference Genome Filepublic java.lang.Boolean includeRareAlleles()
Include the rare alleles at site (3 or 4th states)
public DiscoverySNPCallerPlugin includeRareAlleles(java.lang.Boolean value)
Set Include Rare Alleles. Include the rare alleles at site (3 or 4th states)
value - Include Rare Allelespublic java.lang.Boolean includeGaps()
Include sites where major or minor allele is a GAP
public DiscoverySNPCallerPlugin includeGaps(java.lang.Boolean value)
Set Include Gaps. Include sites where major or minor allele is a GAP
value - Include Gapspublic java.lang.Boolean callBiallelicSNPsWithGap()
Include sites where the third allele is a GAP (mutually exclusive with inclGaps)
public DiscoverySNPCallerPlugin callBiallelicSNPsWithGap(java.lang.Boolean value)
Set Call Biallelic SNPs with Gap. Include sites where the third allele is a GAP (mutually exclusive with inclGaps)
value - Call Biallelic SNPs with Gappublic java.lang.Integer startChromosome()
Start Chromosome
public DiscoverySNPCallerPlugin startChromosome(java.lang.Integer value)
Set Start Chromosome. Start Chromosome
value - Start Chromosomepublic java.lang.Integer endChromosome()
End Chromosome
public DiscoverySNPCallerPlugin endChromosome(java.lang.Integer value)
Set End Chromosome. End Chromosome
value - End Chromosomepublic javax.swing.ImageIcon getIcon()
public java.lang.String getButtonName()
public java.lang.String getToolTipText()
public void discoverSNPsOnChromosome(int targetChromo,
java.io.DataOutputStream locusLogDOS)
public static java.util.HashMap<java.lang.String,java.lang.Double> readTaxaFsFromFile(java.io.File pedigreeFile)
public static byte getIUPACAllele(byte allele)
public static java.lang.String revComplement(java.lang.String seq)