A method for detecting an internal tandem duplication in an FLT3 gene of a sample, comprising: a) 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 of exons of the FLT3 gene; b) sequencing the amplicons to generate a plurality of reads; c) mapping the reads to a reference sequence, wherein the reference sequence includes the targeted regions of exons of the FLT3 gene, wherein the mapping produces a pileup comprising a plurality of alignments of the reads with the reference sequence and a plurality of columns corresponding to positions along the reference sequence, wherein a portion of the plurality of reads are partially mapped to the reference sequence for a plurality of partially mapped reads, wherein a partially mapped read includes a mapped portion, a soft-clipped portion and a breakpoint; d) analyzing the partially mapped reads intersecting a column of the pileup for tandem duplications, including: I. detecting a duplication in the soft-clipped portion by comparing the soft-clipped portion to the mapped portion adjacent to the breakpoint; II. determining an insert size of the duplication in the soft-clipped portion; III. assigning the partially mapped read to a category based on the insert size to generate a plurality of categories corresponding to a plurality of insert sizes, each category having a number of members corresponding to the partially mapped reads having the corresponding insert size; IV. converting the categories into features corresponding to the column, wherein a feature includes the insert size and a sequence of an insert at an insert position; and V. merging the features corresponding to one or more columns representing a same insert to determine a location and a size of a tandem duplication. a) 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 of exons of the FLT3 gene; b) sequencing the amplicons to generate a plurality of reads; c) mapping the reads to a reference sequence, wherein the reference sequence includes the targeted regions of exons of the FLT3 gene, wherein the mapping produces a pileup comprising a plurality of alignments of the reads with the reference sequence and a plurality of columns corresponding to positions along the reference sequence, wherein a portion of the plurality of reads are partially mapped to the reference sequence for a plurality of partially mapped reads, wherein a partially mapped read includes a mapped portion, a soft-clipped portion and a breakpoint; d) analyzing the partially mapped reads intersecting a column of the pileup for tandem duplications, including: I. detecting a duplication in the soft-clipped portion by comparing the soft-clipped portion to the mapped portion adjacent to the breakpoint; II. determining an insert size of the duplication in the soft-clipped portion; III. assigning the partially mapped read to a category based on the insert size to generate a plurality of categories corresponding to a plurality of insert sizes, each category having a number of members corresponding to the partially mapped reads having the corresponding insert size; IV. converting the categories into features corresponding to the column, wherein a feature includes the insert size and a sequence of an insert at an insert position; and V. merging the features corresponding to one or more columns representing a same insert to determine a location and a size of a tandem duplication. I. detecting a duplication in the soft-clipped portion by comparing the soft-clipped portion to the mapped portion adjacent to the breakpoint; II. determining an insert size of the duplication in the soft-clipped portion; III. assigning the partially mapped read to a category based on the insert size to generate a plurality of categories corresponding to a plurality of insert sizes, each category having a number of members corresponding to the partially mapped reads having the corresponding insert size; IV. converting the categories into features corresponding to the column, wherein a feature includes the insert size and a sequence of an insert at an insert position; and V. merging the features corresponding to one or more columns representing a same insert to determine a location and a size of a tandem duplication.