Systems and methods for aligning sequences to personalized references

A system, comprising:

• at least one hardware processor;
• and
• at least one non-transitory computer-readable storage medium storing processor-executable instructions that, when executed by the at least one hardware processor, cause the at least one hardware processor to perform:
• obtaining a plurality of sequence reads for an individual;
• obtaining information identifying a plurality of locations;
• genotyping the plurality of sequence reads for the plurality of locations to obtain a first set of variants for the individual for at least some of the plurality of locations;
• identifying a second set of variants associated with the first set of variants;
• generating a personalized reference sequence construct using the second set of variants;
• and
• aligning the plurality of sequence reads to the personalized reference sequence construct.