Running BayesTyper on other organisms

BayesTyper has been developed with human data in mind, however there is no theoretical problem with running BayesTyper on data from other organisms. When running on other organisms please be aware of the following:

• By default BayesTyper assumes human ploidy levels. This can be changed using --chromosome-ploidy-file in bayesTyper genotype. The chromosome ploidy file should contain three tab-seperated columns (<chromosome_name>, <female_ploidy> & <male_ploidy>) with one line for each chromosome and no header (example). Ploidy levels 0, 1 (haploid) and 2 (diploid) are supported.
• The decoy reference file should contain all chromosomes were the ploidy is unknown such as mitochondrial or unplaced contigs (unless they are known to be autosomal). Also remove all alternative contigs from both the genome and decoy reference file.
• We recommend that you do not filter the candidate variants prior to running BayesTyper.
• The candidate variants should contain SNVs, indels and structural variants. Include already known variants if available for the organism. For structural variants include only variants with breakpoint resolution.
• Use the joint noise genotyping mode (--noise-genotyping) if only genotyping a few candidate variants (< 100,000).