A method for detecting large rearrangements in BRCA1 and BRCA2 genes, comprising: amplifying a nucleic acid sample in the presence of a primer pool to produce a plurality of amplicons, the primer pool including a plurality of target specific primers targeting regions exons of the BRCA1 and BRCA2 genes, wherein the target-specific primers for a region of an exon produce overlapping amplicons that cover the exon; sequencing the amplicons to generate a plurality of reads; mapping the reads to a reference sequence, wherein the reference sequence includes the BRCA1 and BRCA2 genes; determining a number of reads per amplicon for the amplicons associated with the exons of the BRCA1 gene and a number of reads per amplicon for the amplicons associated with the exons of the BRCA2 gene; dividing the number of reads per amplicon for amplicons associated with exons of the BRCA1 gene by a total number of reads of the amplicons generated from the nucleic acid sample to form normalized read counts per amplicon for the BRCA1 gene; dividing the number of reads per amplicon for amplicons associated with exons of the BRCA2 gene by a total number of reads of the amplicons generated from the nucleic acid sample to form normalized read counts per amplicon for the BRCA2 gene; determining exon copy numbers for the exons of the BRCA1 and BRCA2 genes based on the number of reads per amplicon for the amplicons associated with the exons of the BRCA1 and BRCA2 genes; wherein the determining exon copy numbers further comprises comparing the normalized read counts per amplicon and a baseline coverage for the associated exon to determine a candidate copy number for the exon; applying a scaling procedure to the candidate copy numbers for amplicons generated from a germline sample, the scaling procedure comprising: selecting the BRCA1 or BRCA2 gene having a maximum candidate copy number value; determining a median value of the candidate copy number values for exons of the selected gene; setting the median value to a reference level; scaling the candidate copy numbers of the exons of both genes relative to the reference level; detecting an exon deletion or an exon duplication based on the exon copy numbers; and detecting a whole gene deletion of the BRCA1 gene or the BRCA2 gene based on the number of reads per amplicon for the amplicons associated with the exons of the BRCA1 and BRCA2 genes. amplifying a nucleic acid sample in the presence of a primer pool to produce a plurality of amplicons, the primer pool including a plurality of target specific primers targeting regions exons of the BRCA1 and BRCA2 genes, wherein the target-specific primers for a region of an exon produce overlapping amplicons that cover the exon; sequencing the amplicons to generate a plurality of reads; mapping the reads to a reference sequence, wherein the reference sequence includes the BRCA1 and BRCA2 genes; determining a number of reads per amplicon for the amplicons associated with the exons of the BRCA1 gene and a number of reads per amplicon for the amplicons associated with the exons of the BRCA2 gene; dividing the number of reads per amplicon for amplicons associated with exons of the BRCA1 gene by a total number of reads of the amplicons generated from the nucleic acid sample to form normalized read counts per amplicon for the BRCA1 gene; dividing the number of reads per amplicon for amplicons associated with exons of the BRCA2 gene by a total number of reads of the amplicons generated from the nucleic acid sample to form normalized read counts per amplicon for the BRCA2 gene; determining exon copy numbers for the exons of the BRCA1 and BRCA2 genes based on the number of reads per amplicon for the amplicons associated with the exons of the BRCA1 and BRCA2 genes; wherein the determining exon copy numbers further comprises comparing the normalized read counts per amplicon and a baseline coverage for the associated exon to determine a candidate copy number for the exon; applying a scaling procedure to the candidate copy numbers for amplicons generated from a germline sample, the scaling procedure comprising: selecting the BRCA1 or BRCA2 gene having a maximum candidate copy number value; determining a median value of the candidate copy number values for exons of the selected gene; setting the median value to a reference level; scaling the candidate copy numbers of the exons of both genes relative to the reference level; detecting an exon deletion or an exon duplication based on the exon copy numbers; and detecting a whole gene deletion of the BRCA1 gene or the BRCA2 gene based on the number of reads per amplicon for the amplicons associated with the exons of the BRCA1 and BRCA2 genes.