Abstract: Presented herein are systems and methods for identifying splice variants. The techniques include determining one or more sample splice junctions from a plurality of RNA sequence reads from a single biological sample, retrieving a set of baseline splice junctions determined from a plurality of healthy RNA samples and comparing the one or more sample splice junctions to the set of baseline splice junctions to identify one or more filtered sample splice junctions comprising sample splice junctions that do not overlap with the baseline splice junctions, wherein the one or more filtered sample splice junctions are candidate oncogenic events.

Abstract: Methods and systems are provided for validating variant calls. Sequencing data is received for a sample read along the genomic sequence of interest. An indication is received of a potential variant call at a designated position within the sequence of nucleotides along the genomic sequence of interest. The methods and systems obtain baseline variant frequencies at the designated position within one or more baseline genomic sequences, determine a sample variant frequency at the designated position for the genomic sequence of interest, analyze the baseline and sample variant frequencies at the designated position to obtain a quality score, and validate the potential variant call for the genomic sequence of interest based on the quality score.

Abstract: Sequencing data read realignment. A method obtains from a sequence alignment dataset an initial alignment of a read sequence to a reference sequence and performs realignment processing on the initial alignment. The realignment processing includes identifying candidate indel(s) that include zero or more indels in the aligned read and zero or more indels aligned proximal to the aligned read as indicated by the sequence alignment dataset, creating a flattened aligned read based at least on removing from the aligned read any indels indicated by the initial alignment, and determining candidate realignment(s) of the read sequence to the reference sequence based on introducing, for each candidate realignment of the candidate realignment(s), a respective at least one candidate indel of the candidate indel(s) into the flattened aligned read. The method further provides the initial alignment or a selected candidate realignment of the candidate realignment(s) based on selection criteria.