Genotyping by RNA Sequencing

  • GBRS is a suite of tools which includes pseudo-genome creation, allele- specific transcript estimation, and haplotype reconstruction.
  • Users who have J:DO data and work at The Jackson Laboratory can use reference data stored on the high-performance computing cluster.
  • Users outside of The Jackson Laboratory will need to create or download the reference files.

Installing GBRS

  • GBRS requires support software and Diversity Outbred reference files to run.
  • GBRS uses nextflow to run the GBRS pipeline.
  • GBRS uses a container system, either docker or Singularity, to modularize required software versions.
  • Diversity Outbred (DO) reference files are needed to run GBRS on DO mice.

Running GBRS

  • GBRS produces several output file for each sample.

Preparing GBRS Pseudo-References

  • Use the default nextflow pipeline if working with DO mice on sumner2.
  • You can query the VCFs and get the strain names using tabix.
  • You can specify another set of strains and use the default reference genome.
  • Advanced users can run the pipeline line-by-line and specify different options.

Prepare EMASE Reference Files