public class ProductionSNPCallerPlugin
extends AbstractPlugin
This plugin converts all of the fastq (and/or qseq) files in the input folder and keyfile to genotypes and adds these to a genotype file in HDF5 format. We refer to this step as the "Production Pipeline". The output format is HDF5 genotypes with allelic depth stored. SNP calling is quantitative with the option of using either the Glaubitz/Buckler binomial method (pHet/pErr > 1 = het) (=default), or the Stacks method. Merging of samples with the same LibraryPrepID is handled by GenotypeTableBuilder.addTaxon(), with the genotypes re-called based upon the new depths. Therefore, if you want to keep adding genotypes to the same target HDF5 file in subsequent runs, use the -ko (keep open) option so that the output GenotypeTableBuilder will be mutable, using closeUnfinished() rather than build(). If the target output HDF5 GenotypeTable file doesn't exist, it will be created. Each taxon in the HDF5 file is named "ShortName:LibraryPrepID" and is annotated with "Flowcell_Lanes" (=source seq data for current genotype). Requires a TOPM with variants added from a previous "Discovery Pipeline" run. In binary topm or HDF5 format (TOPMInterface). TODO add the Stacks likelihood method to BasicGenotypeMergeRule
public static java.lang.String rawSeqFileNameRegex
public ProductionSNPCallerPlugin()
public ProductionSNPCallerPlugin(java.awt.Frame parentFrame,
boolean isInteractive)
public void postProcessParameters()
public javax.swing.ImageIcon getIcon()
public java.lang.String getButtonName()
public java.lang.String getToolTipText()
public java.lang.String inputDirectory()
Input directory containing fastq AND/OR qseq files.
public ProductionSNPCallerPlugin inputDirectory(java.lang.String value)
Set Input Directory. Input directory containing fastq AND/OR qseq files.
value - Input Directorypublic java.lang.String keyFile()
Key file listing barcodes distinguishing the samples
public ProductionSNPCallerPlugin keyFile(java.lang.String value)
Set Key File. Key file listing barcodes distinguishing the samples
value - Key Filepublic java.lang.String enzyme()
Enzyme used to create the GBS library
public ProductionSNPCallerPlugin enzyme(java.lang.String value)
Set Enzyme. Enzyme used to create the GBS library
value - Enzymepublic java.lang.String inputTOPMFile()
Physical map file containing tags and corresponding variants (production TOPM)
public ProductionSNPCallerPlugin inputTOPMFile(java.lang.String value)
Set Input TOPM File. Physical map file containing tags and corresponding variants (production TOPM)
value - Input TOPM Filepublic java.lang.String outputHDF5GenotypesFile()
Output (target) HDF5 genotypes file to add new genotypes to (new file created if it doesn't exist)
public ProductionSNPCallerPlugin outputHDF5GenotypesFile(java.lang.String value)
Set Output HDF5 Genotypes File. Output (target) HDF5 genotypes file to add new genotypes to (new file created if it doesn't exist)
value - Output HDF5 Genotypes Filepublic java.lang.Double aveSeqErrorRate()
Average sequencing error rate per base (used to decide between heterozygous and homozygous calls)
public ProductionSNPCallerPlugin 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.Boolean keepGenotypesOpen()
Keep hdf5 genotypes open for future runs that add more taxa or more depth
public ProductionSNPCallerPlugin keepGenotypesOpen(java.lang.Boolean value)
Set Keep Genotypes Open. Keep hdf5 genotypes open for future runs that add more taxa or more depth
value - Keep Genotypes Openpublic java.lang.Boolean noDepthToOutput()
No depth output: do not write depths to the output hdf5 genotypes file
public ProductionSNPCallerPlugin noDepthToOutput(java.lang.Boolean value)
Set No Depth to Output. No depth output: do not write depths to the output hdf5 genotypes file
value - No Depth to Output