Determining structural variants

A system for identifying structural variants in a polynucleotide, comprising:

• a memory;
• and
• at least one processor configured to perform a method, comprising:
• obtaining sequence reads from a flowcell comprising fragments of a polynucleotide, wherein a probability of the fragments of the polynucleotide being located near each other on the flowcell is correlated with a distance between the fragments of the polynucleotide in the polynucleotide;
• determining anchor sequence reads flanking putative structural variants in the polynucleotide;
• and
• identifying structural variants in the polynucleotide by analyzing sequence reads located within a threshold distance to the anchor sequence reads on the flowcell to determine sequence reads linked to the anchor sequence reads.