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SCRIPT PURPOSE

Generate reference intervals for the Practical Haplotype Graph (PHG)

NOTES

This script assumes it is run inside the PHG Docker container with predefined I/O paths
The .gff file is assumed to be in JGI format: gene models have the "gene" name, and an "ID=..." field is present in annotation

RUNNING THE SCRIPT

#!bash

docker run --rm                                                                    \
-v /your_data_folder/:/tempFileDir/data                                            \
maizegenetics/phg                                                                  \
/CreateReferenceIntervals.sh -f your_reference.fasta -a your_reference.gene.gff3 [ ... optional parameters]

REQUIRED PARAMETERS

#!bash

   -f <file name>  
      name of fasta file containing the reference sequence  
   -a <file name>  
      name of genome annotation file in .gff format containing gene model annotation

OPTIONAL PARAMETERS

#!bash

  -k <integer>  
     Length of kmer used for determining repetitive regions  
     Default: 11
  -e <integer>  
     Number of bases by which to expand gene models for initial reference interval selection  
     Default: 1000
  -m <integer>  
     Distance (in bp) between genes below which gene models are merged  
     Default: 100
  -p <double>  
     Proportion of kmers to be considered repetitive.  
     This determines the high kmer count tail which is considered repetitive (e.g. the top 0.05 most frequent)  
     Default: 0.1
  -n <integer>  
     Number of kmer copies (genome-wide) above which a kmer is considered repetitive. Overrides -p  
     Default: none, -p is used by default
  -l <integer>  
     The number of bases to consider when evaluating if a location in the genome is repetitive  
     Default: 100
  -s <integer>  
     The step size (in bp) by which to proceed outward from a gene model when evaluating flanking regions  
     Default: 10

SCRIPT RESULTS

Output location (subfolder in the input data folder)

genomic_intervals_unique-timestamp

Relevant output contents

reference_intervals_run.log -- a log file summarizing parameters for the run
your_fasta.gene.expand.trimmed.summary_report.tsv -- a summary of seed gene model expansion
your_fasta.kmer_count.tsv -- a complete list of kmer counts for kmers with count > 1
your_fasta.gene.expand.trimmed.bed -- the final reference intervals, in BED format