Methods, systems, and computer-readable media for calculating corrected amplicon coverages

A system for calculating corrected amplicon coverages, the system including:

• a data storage device that stores instructions system for calculating corrected amplicon coverages;
• and
• a processor configured to execute the instructions to perform a method including:
• mapping a plurality of reads of a plurality of amplicons based on amplified target regions of a sample suspected of having one or more genetic abnormalities to a reference sequence, the reference sequence including one or more nucleic acid sequences corresponding to the amplified target regions;
• calculating amplicon coverages and total reads, wherein amplicon coverages is a number of reads mapped to an amplicon, and total reads is a number of mapped reads;
• and
• calculating corrected amplicon coverages based on the calculated amplicon coverages and calculated total reads by applying a batch effect correction.

A non-transitory computer-readable medium storing instructions that, when executed by a computer, cause the computer to perform a method for calculating corrected amplicon coverages, the method including:

• mapping a plurality of reads of a plurality of amplicons based on amplified target regions of a sample suspected of having one or more genetic abnormalities to a reference sequence, the reference sequence including one or more nucleic acid sequences corresponding to the amplified target regions;
• calculating amplicon coverages and total reads, wherein amplicon coverages is a number of reads mapped to an amplicon, and total reads is a number of mapped reads;
• and
• calculating corrected amplicon coverages based on the calculated amplicon coverages and calculated total reads by applying a batch effect correction.