Preparing a new genome index for sarek

Requirement

• fasta sequence of custom genome/genome scaffolds

Two-staged process (source: Craig Windell)

Run1:

• The first time running sarek specify the custom fasta file (--fasta mygenome.fa) and add the option to save reference sequence (--save_reference)

  • Sarek will generate a bed, BWAIndex files etc it saved them to the results folder.

  • Copy generated files to reference folder and updated the qutgenomes.config file

Run 2:

• sarek pipeline is run using generated files in run1