A pipeline to identify clonal lymphocyte populations from paired-end RNA sequencing reads, with a primary focus on sequencing mRNA from neoplastic cells. VDJSeq-Solver detects the main clone for the tissue of interest by capturing the most abundant V(D)J junction among the existing ones. It is able to characterize the V(D)J rearrangement by obtaining the exact sequence of the main clone. VDJSeq-Solver overcomes limitations of currently available lymphocyte rearrangements recognition methods that are designed to work with amplicon sequencing data and perform badly in case of irregular junction coverage. It was shown to correctly identify the main clone in case of five Mantle Cell Lymphoma samples and was further successfully tested on twelve Diffuse Large B-Cell Lymphoma samples.