METHOD AND APPARATUS FOR CALLING SINGLE-NUCLEOTIDE VARIATIONS AND OTHER VARIATIONS

摘要

Base calls for a target sequence may be identified relative to a reference sequence by using values from sequencing reads at locations satisfying a high-confidence condition to identify base calls at a given location not satisfying the high-confidence condition. The high-confidence condition may relate to the level of coverage by the sequencing reads at a location of the reference sequence. The quality of measurements of the sequencing reads may be incorporated into the base-call process.

主权项

1. A method of identifying at least one base call for a target sequence, the method comprising:
accessing the reference sequence, the reference sequence including a plurality of base values that define the reference sequence; accessing a plurality of sequencing reads, each sequencing read including a plurality of base values for a corresponding portion of the target sequence; identifying a plurality of high-confidence locations in the sequencing reads, a high-confidence location being identified with a corresponding location in the reference sequence and satisfying a high-confidence condition for using base values of the sequencing reads at the high-confidence location to identify one or more base calls for the target sequence at the high-confidence location; and identifying one or more base calls for the target sequence at a given location not satisfying the high-confidence condition by using base values of the sequencing reads at the high-confidence locations with base values of the sequencing reads at the given location and a base value of the reference sequence at the given location to identify the one or more base calls for the target sequence at the given location.