This section describes the model, method and estimation procedure behind the Low Frequency Variant caller. The Low Frequency variant caller is designed to detect variants in a sample for which the ploidy is unknown. The low Frequency variant caller has a particularly high sensitivity for detecting variants that are present at any, and in particularly at low, allele frequencies.
- The Low Frequency Variant caller
- The model for the Low Frequency Variant Caller
- Updating the choice of favored Multinomial model for each site
- Updating equations for the error rates