A computer-implemented method for calling variations in a sample polynucleotide sequence with respect to a reference polynucleotide sequence, the method comprising: receiving the reference polynucleotide sequence and mapped mated reads, wherein the mapped mated reads are obtained from the sample polynucleotide sequence and are mapped to locations in the reference polynucleotide sequence; locating local areas (300, 502) in the reference polynucleotide sequence where a likelihood that one or more bases of the sample polynucleotide sequence are changed from corresponding bases in the reference polynucleotide sequence exceeds a likelihood threshold, where the likelihood of a local area is determined at least in part based on a number of the mapped mated reads of the sample polynucleotide sequence that map to the local area and that have a base that varies from the reference polynucleotide sequence in the local area, wherein locating the local areas likely to have changed from the reference further comprises computing local de novo intervals using a partial de Bruijn graph to find variations beyond single base changes; generating at least one sequence hypothesis for each of the local areas, each sequence hypothesis including a respective base used to determine the likelihood that exceeds the likelihood threshold; optimizing the at least one sequence hypothesis for at least a portion of the local areas to find one or more optimized sequence hypotheses, the optimizing including: changing one or more bases of the at least one sequence hypothesis to find the one or more optimized sequence hypotheses that have an increased probability for the local areas based on the number of mapped mated reads that map to the local areas; and analyzing the optimized sequence hypotheses in relation to the reference polynucleotide sequence to identify a series of variation calls in the sample polynucleotide sequence. receiving the reference polynucleotide sequence and mapped mated reads, wherein the mapped mated reads are obtained from the sample polynucleotide sequence and are mapped to locations in the reference polynucleotide sequence; locating local areas (300, 502) in the reference polynucleotide sequence where a likelihood that one or more bases of the sample polynucleotide sequence are changed from corresponding bases in the reference polynucleotide sequence exceeds a likelihood threshold, where the likelihood of a local area is determined at least in part based on a number of the mapped mated reads of the sample polynucleotide sequence that map to the local area and that have a base that varies from the reference polynucleotide sequence in the local area, wherein locating the local areas likely to have changed from the reference further comprises computing local de novo intervals using a partial de Bruijn graph to find variations beyond single base changes; generating at least one sequence hypothesis for each of the local areas, each sequence hypothesis including a respective base used to determine the likelihood that exceeds the likelihood threshold; optimizing the at least one sequence hypothesis for at least a portion of the local areas to find one or more optimized sequence hypotheses, the optimizing including: changing one or more bases of the at least one sequence hypothesis to find the one or more optimized sequence hypotheses that have an increased probability for the local areas based on the number of mapped mated reads that map to the local areas; and analyzing the optimized sequence hypotheses in relation to the reference polynucleotide sequence to identify a series of variation calls in the sample polynucleotide sequence. changing one or more bases of the at least one sequence hypothesis to find the one or more optimized sequence hypotheses that have an increased probability for the local areas based on the number of mapped mated reads that map to the local areas; and analyzing the optimized sequence hypotheses in relation to the reference polynucleotide sequence to identify a series of variation calls in the sample polynucleotide sequence.