Methods for analyzing nucleic acids

A method, comprising:

• (a) providing a first polynucleotide and a second polynucleotide, wherein the first polynucleotide and the second polynucleotide are linked, wherein the second polynucleotide is at least partially complementary to the first polynucleotide, and wherein the first polynucleotide comprises at least a portion of a genomic polynucleotide;
• (b) contacting the first polynucleotide and the second polynucleotide with an agent that specifically glycosylates 5-hydroxymethylcytosine (5-hmC);
• (c) determining sequences of the first polynucleotide and the second polynucleotide to determine a first identity of a first base at a locus of the first polynucleotide and a second identity of a second base at a corresponding locus of the second polynucleotide using sequencing;
• and
• (d) using a computer comprising a processor, a memory, and instructions stored thereupon that, when executed, determine an identity of a true base of the genomic polynucleotide corresponding to the locus of the first polynucleotide based at least in part on the identity of the first base and the identity of the second base.