Software Packages

Department of Quantitative Health Sciences
Mayo Clinic Research
Formerly known as the Department of Health Sciences Research

Related links: Division Overview R Shiny Applications

GenomeSmasher SV_generator description

SV_generator. sh is a useful shell script that calls several perl scripts that help to generate structural variations to insert into a synthetic genome.

Usage

Usage: SV_Generator.sh

The inputs are defined below:

  • SCRIPTS_DIR
    • The scripts directory is the full path to a series of perl scripts that will generate different types of structural variations:
      1. Copy_number_changes.pl
      2. Inversions.pl
      3. Large_Deletions.pl
      4. Novel_insertions.pl
      5. Translocations.pl
  • Genome_DIR
    • The scripts directory is a directory that contains chromosome files for an individual reference genome assembly. They must be stored by chromosome, beginning with “chr” and ending with “.fa”.
  • OUTPUT_VCF
    • This is the name of the final vcf-like file to create
  • NUM_BASES_FASTAFILE_EACHLINE
    • some FAST files are 60 nucleotides long, whereas others are 50. Make sure to select the corresponding length for your reference FASTA file inputs.

Special Notes

No mutations will be added if the nucleotide where the event is being inserted is “N”.

Page last modified: October 24, 2014