A computer-implemented method for identifying a copy number variation based on corrected amplicon coverages, the method comprising: obtaining a plurality of reads generated from a training sample, wherein the training sample includes a normal sample having a known ploidy; mapping the plurality of training reads to a nucleic acid reference sequence; calculating amplicon coverages and total reads for the training sample, wherein an amplicon coverage is a number of reads mapped to an amplicon and the total reads is a number of mapped reads; determining values for multiple batch effects that jointly affect the training sample and a scaling factor by applying a principal components analysis to the amplicon coverages calculated for the training sample, wherein each principal component represents a vector of values for one batch effect; obtaining a plurality of reads of a plurality of amplicons based on amplified target regions of a test sample having an unknown ploidy; mapping the plurality of reads 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 for the test sample; determining a sample dependent scaling factor by applying a principal components analysis to the amplicon coverages calculated for the test sample; calculating corrected amplicon coverages by applying a batch effect correction based on the calculated amplicon coverages for the test sample, the sample dependent scaling factor determined for the test sample and the batch effect values determined for the training sample; and identifying the copy number variation of the test sample based on the calculated corrected amplicon coverages. obtaining a plurality of reads generated from a training sample, wherein the training sample includes a normal sample having a known ploidy; mapping the plurality of training reads to a nucleic acid reference sequence; calculating amplicon coverages and total reads for the training sample, wherein an amplicon coverage is a number of reads mapped to an amplicon and the total reads is a number of mapped reads; determining values for multiple batch effects that jointly affect the training sample and a scaling factor by applying a principal components analysis to the amplicon coverages calculated for the training sample, wherein each principal component represents a vector of values for one batch effect; obtaining a plurality of reads of a plurality of amplicons based on amplified target regions of a test sample having an unknown ploidy; mapping the plurality of reads 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 for the test sample; determining a sample dependent scaling factor by applying a principal components analysis to the amplicon coverages calculated for the test sample; calculating corrected amplicon coverages by applying a batch effect correction based on the calculated amplicon coverages for the test sample, the sample dependent scaling factor determined for the test sample and the batch effect values determined for the training sample; and identifying the copy number variation of the test sample based on the calculated corrected amplicon coverages.