Models for Targeted Sequencing

A computer-product comprising a computer readable medium storing a plurality of instructions for controlling a computer system to:

• generating a plurality of candidate variants of a cell free nucleic acid sample;
• determining likelihoods of true alternate frequencies for each of the candidate variants in the cell free nucleic acid sample and in a corresponding genomic nucleic acid sample;
• filtering the candidate variants at least by a model using the likelihoods of true alternate frequencies;
• and
• outputting the filtered candidate variants.

A system comprising a computer processor and a memory, the memory storing computer program instructions that when executed by the computer processor cause the processor to perform steps comprising:

• generating a plurality of candidate variants of a cell free nucleic acid sample;
• determining likelihoods of true alternate frequencies for each of the candidate variants in the cell free nucleic acid sample and in a corresponding genomic nucleic acid sample;
• filtering the candidate variants at least by a model using the likelihoods of true alternate frequencies;
• and
• outputting the filtered candidate variants.