FASTQ to hap count plugin

Legacy Documentation - PHG Version 1

This section contains documentation for PHG version 1, which is no longer actively developed. It is preserved here for archival and historical reference only. If you are looking to use the Practical Haplotype Graph, please refer to the PHG v2 documentation, which reflects the current version of the software.

The FastqToHapCountPlugin executes code to count the number of reads which align to a haplotype node. It scores which haplotypes are identical, excluded, or unresolved relative to a perfect hit GenotypeMap. The plugin requires a PHG Haplotype Graph, which can be acquired by chaining the running of HaplotypeGraphBuilderPlugin and this plugin. The output from the HaplotypeGraphBuilderPlugin will be input to the FastqToHapCountPlugin. For example:

#!java
     /tassel-5-standalone/run_pipeline_jbwa.pl -Xmx5g -debug -HaplotypeGraphBuilderPlugin 
          -configFile $CONFIGFILE -onlyAnchors true -consensusMethod $CONSENSUS_METHOD 
          -includeVariantContexts true -endPlugin 
          -FastqToHapCountPlugin -taxon $file -configFile $CONFIGFILE -haplotypeFile $HAPLOTYPE_FASTA 
          -method $HAP_COUNT_METHOD -version $VERSION -refFile $REFERENCE_FILE 
          -rawReadFile ${FASTQ_DIR}/${file}.fastq -exportHaploFile ${FASTQ_HAP_COUNT_DIR}/${file}.txt

The parameters for this plugin are:

• -configFile DB Config File containing properties host,user,password,DB and DBtype where DBtype is either sqlite or postgres (Default=null) (REQUIRED) A sample config file can be found here:Config File Wiki.
• -haplotypeFile Fasta file and associated BWA indices for haplotypes stored in the PHG db. (Default=null) (REQUIRED)
• -refFile Reference genome file - temporary need until we can back convert coordinates. (Default=null) (REQUIRED)
• -rawReadFile Raw Read file aligned to the reference. (Default=null) (REQUIRED)
• -exportHaploFile Text file to store haplotype scoring. (Default=null) (OPTIONAL)
• -taxon Taxon name to load into genotypes table from linked plugin. (Default=null) (REQUIRED)
• -debugTaxon Used for debugging. (Defaulg=null) (OPTIONAL)
• -method Name of method used to create hap counts, for the haplotype_counts table. (Default=null) (REQUIRED)
• -version Genome intervals version name as stored in the PHG db genome_intervals_version table. (Default=null) (REQUIRED)
• -loadDB Whether to populate the haplotype_counts table. Should be true unless user is testing. (Default=true) (OPTIONAL)

Once the haplotype counts have been determined, they are loaded to the database if the loadDB flag is "true"..