Patent Document ID: 9499863
Application ID: 14028319
Patent Flag: 1

Claim One:
1. A method of analyzing genomic DNA in a sample, the method comprising: (a) dividing the sample into a plurality of separate aliquots; (b) amplifying fragments of the genomic DNA in the separate aliquots to produce a plurality of amplicons, wherein the amplifying is conducted with a population of dNTPs containing dNTP analogs, whereby a number of nucleotides in the amplicons are nucleotide analogs; (c) removing nucleotide analogs incorporated into the amplicons to form gapped DNA; (d) treating the gapped DNA such that gaps on opposite strands converge, thereby further fragmenting the genomic DNA; (e) tagging DNA fragments in different aliquots with different oligonucleotide tags or tag combinations to form tagged fragments; (f) combining the aliquots to produce a mixture of tagged fragments; (g) obtaining sequence reads from tagged fragments in the mixture, wherein using the nucleotide analogs to create the gapped DNA has the effect of reducing GC bias in the sequence reads; and (h) phasing heterozygous loci in the genomic DNA by a process that includes identifying sequence reads for DNA fragments having the same oligonucleotide tag.