Methods and systems for genotyping genetic samples

Abstract

The invention provides methods and system for making specific base calls at specific loci using a reference sequence construct, e.g., a directed acyclic graph (DAG) that represents known variants at each locus of the genome. Because the sequence reads are aligned to the DAG during alignment, the subsequent step of comparing a mutation, vis-a-vis the reference genome, to a table of known mutations can be eliminated. The disclosed methods and systems are notably efficient in dealing with structural variations within a genome or mutations that are within a structural variation.

Description

[0001] related application [0002] This application claims priority to US Patent Application Serial No. 61 / 892,662, filed October 18, 2013, which is incorporated herein by reference in its entirety. technical field [0003] The present invention relates to methods and systems for genotyping genetic samples. Background technique [0004] Advances in sequencing technology have made it possible to sequence an individual's genome in a week or less. Typically, genetic samples are isolated, fragmented, amplified and subsequently analyzed in, for example, Illumina TM Sequencing (Illumina, Inc., San Diego, CA) on a High Throughput System. This process generates a large number of sequence reads, which must then be combined to generate a sequence. The sequences themselves provide little useful information, however, because the diagnostic and predictive value of the information depends on the relative position of the sequences in the genome. That is, it is only possible to determ...

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Problems solved by technology

In other words, current methods do not fully represent structural variation that is often seen in many genomes

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