High-fault-tolerance genome complex structure variation detection method based on filtering strategy

Abstract

The invention discloses a high-fault-tolerance genome complex structure variation detection method based on a filtering strategy, and the method comprises the steps: carrying out preprocessing on an input file in an SAM format, and traversing a CIGAR field in an optimal quality comparison reading segment; according to the compared CIGAR field and variation score calculation criterion, calculatinga variation score corresponding to each site in the current reading segment, and storing the variation score in a variation score set of each site in advance; counting an average value in the variation score set of each site as a final variation score of the site and obtaining a variation score function of the sample; carrying out Kalman or Gaussian filtering on the variation score function to obtain a variation score function after filtering and noise reduction; according to the filtered variation score function, setting a threshold value and separating a structure variation region, and carrying out feature extraction; and training a support vector machine (SVM) model, and classifying the structural variation regions by using the trained SVM model to obtain a complex indel result set. According to the invention, the interference of sequencing errors on the determination of structural variation is solved.

Description

Technical field [0001] The invention belongs to the technical field of third-generation nucleic acid sequence sequencing (Single Molecule Real Time, SMRT), and specifically relates to a high-fault-tolerant genome mutation detection method based on a filtering strategy. Background technique [0002] Complex insertion-deletion (Complex insertion-deletion) is a genomic structural variation that is relatively rare in the population but more frequently in the tumor genome. A complex indel is a compound mutation in which a DNA fragment of a gene has a deletion mutation. Due to the self-repair mechanism of the DNA molecule, other DNA fragments are subsequently inserted at the same site and the inserted fragments may be inverted. There are dozens of manifestations of complex indels that have been discovered so far. As an important structural variation, the detection of complex indels is the basis for downstream analysis of the correlation between tumor susceptibility and phenotype. Exp...

AI Technical Summary

Problems solved by technology

[0007] The technical problem to be solved by the present invention is to provide a high-error-tolerant genome complex structural variation detection method based on the filtering strategy to solve the interference caused by sequencing errors to the determination of structural variation and solve the impact of sequencing errors on the above-mentioned deficiencies in the prior art. Interference arising from the discrimination of complex indels and other structural variants

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