Method and system for structural variant detection in third generation whole exome sequencing transcript data

Abstract

The application belongs to the technical field of bioinformatics, and relates to a method and system for detecting structural variation in transcript data of three-generation whole-exome sequencing, comprising: establishing a transcript set to be searched for structural variation; mapping and annotating transcript information according to TAGET software, cyclically reading the transcript set, and obtaining first structural variation of all transcripts; mapping transcript information according to Hisat2 software, cyclically reading the transcript set, and obtaining second structural variation of all transcripts; filtering and screening the first structural variation and the second structural variation respectively, and generating screened transcripts of the first structural variation and the second structural variation; and comprehensively screening the screened transcripts of the first structural variation and the second structural variation, and obtaining the final structural variation of the transcripts. The application improves the positive rate of structural variation and greatly reduces false positives by cross comparison of results of two kinds of software and strict control of the difference value of exon breakpoints between the transcript and the reference transcript.

Description

TECHNICAL FIELD

[0001] The present application relates to a method, system and readable medium for detecting structural variation in three-generation whole-exome sequencing transcript data, and belongs to the technical field of bioinformatics. BACKGROUND

[0002] The third-generation sequencing technology refers to single molecule sequencing technology. When sequencing DNA, it does not need to be amplified by PCR, and each DNA molecule is sequenced individually. The third-generation sequencing technology is also called de novo sequencing technology, that is, single molecule real-time DNA sequencing.

[0003] The principle of the third-generation sequencing technology mainly includes two kinds:

[0004] The first is single molecule fluorescent sequencing, and the representative technologies are SMS technology of Helicos in the United States and SMRT technology of Pacific Bioscience in the United States. Deoxynucleotides are labeled with fluorescence, and the intensity change of fluorescence can be recorded in real time by a microscope. When the fluorescently labeled deoxynucleotide is incorporated into the DNA chain, its fluorescence can be detected on the DNA chain at the same time. When it forms a chemical bond with the DNA chain, its fluorescent group is cut off by the DNA polymerase, and the fluorescence disappears. This fluorescently labeled deoxynucleotide does not affect the activity of the DNA polymerase, and after the fluorescence is cut off, the synthesized DNA chain is exactly the same as the natural DNA chain.

[0005] The second is nanopore sequencing, and the representative company is Oxford Nanopore Technologies in the United Kingdom. The new nanopore sequencing method uses electrophoresis technology to drive a single molecule to pass through a nanopore one by one to realize sequencing. Since the diameter of the nanopore is very small, only a single nucleic acid polymer is allowed to pass through, and the electric properties of ATCG single bases are different, the difference in electric signals can be detected to detect the type of passing base, thereby realizing sequencing.

[0006] Compared with the second-generation sequencing, the third-generation whole transcriptome sequencing can completely detect the full-length transcript sequence, so as to capture the transcription start site and splicing site of each transcript, which is convenient for us to more accurately and clearly judge whether the transcript has a structural variation; among the two third-generation sequencing technologies, compared with nanopore sequencing (Nanopore), single molecule fluorescent sequencing (Pacbio) innovatively adds a loop adapter to both sides of a sequence, and uses the long sequencing characteristics to repeatedly sequence the sequence, realizes self-alignment and self-correction among subreads of a sequence, and effectively solves the high error rate of third-generation sequencing. Therefore, the present application selects Pacbio sequencing technology to sequence the sample, which is conducive to more accurately discovering structural variations and reducing non-logical errors caused by sequencing technology. SUMMARY

[0007] In order to solve the above problems, the present application aims to provide a method, system and readable medium for detecting structural variations in transcript data of third-generation whole exome sequencing, which utilizes cross comparison of two software results and strict control of the difference of exon breakpoints between transcripts and reference transcripts, thereby improving the positive rate of structural variations and greatly reducing false positives.

[0008] To achieve the above object, the present application provides the following technical scheme: a method for detecting structural variations in transcript data of third-generation whole exome sequencing, comprising the following steps: establishing a transcript set to be searched for structural variations; mapping and annotating to obtain transcript information according to TAGET software (TAGET software includes mapping and annotation functions, wherein the mapping part is based on three optional software Hisat2, minimap2 and GMAP, and the subsequent analysis in the present application is based on the mapping and annotation results of TAGET, and the configuration file of TAGET is read); reading the transcript set in a loop to obtain the first structural variation of all transcripts; obtaining transcript information by mapping according to Hisat2 software, reading the transcript set in a loop to obtain the second structural variation of all transcripts; filtering and screening the first structural variation and the second structural variation respectively to generate screened transcripts of the first structural variation and the second structural variation; and comprehensively analyzing the screened transcripts of the first structural variation and the second structural variation to obtain the final structural variation of the transcripts.

[0009] Further, the method for establishing the transcript set to be searched for structural variations comprises the following steps: performing third-generation whole transcriptome sequencing on a sample to generate third-generation whole transcriptome sequencing results; mapping the third-generation whole transcriptome sequencing results using TAGET software to obtain third-generation whole transcriptome sequencing annotation information and transcript information; and retaining transcripts that cannot be completely matched with reference sequences according to the annotation information to generate the transcript set to be searched for structural variations.

[0010] Further, the method for obtaining the first structural variation or the second structural variation from the transcript information comprises the following steps: according to the gene annotation information of the transcript, the transcript to be searched for the structural variation is matched with the reference transcript with the annotated gene one by one, if a certain reference transcript is highly similar to the transcript to be searched for the structural variation at the breakpoint and does not have the structural variation feature, it is considered that the transcript to be searched for the structural variation does not have the structural variation; otherwise, all the fuzzy matched reference transcripts are reserved, and a reference transcript set is generated; the transcript to be searched for the structural variation and the reference transcript in the reference transcript set are matched one by one, and whether the transcript to be searched for the structural variation has the structural variation is judged in order; the structural variation of each transcript is screened, and the structural variation closer to the reference transcript and the unique reference transcript are reserved.

[0011] Further, the structural variation comprises a repeat, an inversion and a deletion, and the deletion comprises an intron internal deletion and an exon entire deletion.

[0012] Further, the method for judging whether the transcript to be searched for the structural variation has the structural variation comprises the following steps: according to the breakpoint information of the transcript to be searched for the structural variation, the breakpoint information is matched with the breakpoint information of the reference transcript, the information that the exons contained in the transcript to be searched for the structural variation are mapped to the exon positions on the reference transcript is obtained, whether there are multiple exons in the exons contained in the transcript to be searched for the structural variation that are mapped to the same exon in the reference transcript is judged, if yes, the exons are added to a first exon set, and the mapped reference positions are recorded, whether there are three types of structural variations of the repeat, the inversion and the deletion in the exons in the first exon set is judged, if not, according to the positive and negative strand information in the annotation information, whether the transcript to be searched for the structural variation has the inversion structural variation is judged, if yes, the inversion structural variation and the breakpoint difference and the structural variation start and end points of the corresponding reference transcript are recorded; whether there is an exon entire deletion in the breakpoint information obtained by the transcript to be searched for the structural variation according to the information that the exons contained in the transcript to be searched for the structural variation are mapped to the exon positions on the reference transcript is judged.

[0013] Further, the judging whether the exon in the first exon set has the three types of structural variations of duplication, inversion and deletion comprises the following steps: judging whether the exon in the first exon set has the duplication structural variation, and if yes, recording the duplication structural variation, breakpoint difference of the corresponding reference transcript and start and end points of the structural variation; removing the exon with the duplication structural variation and generating a second exon set; if the second exon set is not empty, judging whether the exon in the second exon set has the deletion structural variation, and if yes, recording the deletion structural variation, breakpoint difference of the corresponding reference transcript and start and end points of the structural variation; judging whether the transcript to be searched for structural variation has the inversion structural variation according to the positive and negative strand information in the annotation information, and recording the inversion structural variation, breakpoint difference of the corresponding reference transcript and start and end points of the structural variation; judging whether the whole exon deletion exists in the breakpoint information of the transcript to be searched for structural variation according to the information that the exon in the transcript to be searched for structural variation is mapped to the exon position of the reference transcript.

[0014] Further, the method for judging whether the whole exon deletion exists in the breakpoint information of the transcript to be searched for structural variation comprises the following steps: taking the exon in the reference transcript to which the first exon in the transcript to be searched for structural variation is mapped as the first exon; taking the exon in the reference transcript to which the last exon in the transcript to be searched for structural variation is mapped as the second exon; and judging whether the exon region between the first exon and the second exon is deleted.

[0015] Further, the method for filtering and screening the first structural variation and the second structural variation respectively comprises the following steps: first, the same transcript cannot have the structural variations mapped to different reference transcripts; second, the exon breakpoint set in the transcript without the structural variation is the same as or similar to the corresponding exon breakpoint set on the reference transcript mapped, and the structural variation with a large breakpoint difference is not collected; third, the deletion structural variation of the transcript must have the reference transcript meeting the standard in the second step; fourth, the duplication and inversion structural variation of the transcript is recorded if the reference gene exists when the deletion exists; and the non-actual existing structural variation of the transcript generated by mapping is reduced.

[0016] The application further discloses a system for detecting structural variation in transcript data of third-generation full-length transcriptome sequencing, comprising: a transcript set establishing module, which is used to establish a transcript set for which structural variation is to be found; a first structural variation obtaining module, which is used to obtain transcript information according to TAGET software mapping, and cyclically read the transcript set to obtain first structural variation of all transcripts; a second structural variation obtaining module, which is used to obtain transcript information according to Hisat2 software mapping, and cyclically read the transcript set to obtain second structural variation of all transcripts; a screening module, which is used to filter and screen the first structural variation and the second structural variation respectively, and generate screened transcripts of the first structural variation and the second structural variation; and an output module, which is used to comprehensively obtain the screened transcripts of the first structural variation and the second structural variation to obtain the final structural variation of the transcripts.

[0017] The application further discloses a computer readable storage medium, wherein a computer program is stored on the computer readable storage medium, and the computer program is executed by a processor to implement the structural variation detection method in transcript data of third-generation full-exon sequencing.

[0018] The application has the following advantages due to the above technical scheme: the detection method for finding structural variation in transcript data established by the application firstly considers the influence of mapping results of different mapping software on finding structural variation, utilizes the characteristics of Hisat2 and minimap2 in the mapping process of TAGET software, finds structural variation of transcripts by respectively finding structural variation of TAGET mapping results and Hisat2 mapping results, and comprehensively screens; compared with finding structural variation by using mapping results of a single mapping software, the application utilizes cross comparison of results of two kinds of software and strict control of difference values of exons between transcripts and reference transcripts, improves the positive rate of structural variation, and greatly reduces false positives. Meanwhile, the application utilizes the characteristics of Hisat2 and minimap2 in the mapping process of TAGET software, is different from the method of obtaining results by using multiple mapping and finding structural variation software and then taking intersection, comprehensively considers the influence of different mapping software on structural variation in the process of finding structural variation, and outputs results, avoids waste of computing resources and time caused by multiple mapping in the traditional method of finding structural variation by using multiple mapping software results, supplements loss of structural variation caused by mapping software algorithms, improves the positive rate of structural variation results, the method established by the application is more economical and efficient in terms of computing resources, and the application has important value in finding structural variation of transcript data. BRIEF DESCRIPTION OF DRAWINGS

[0019] Figure 1is a flow chart of a structural variation detection method in three-generation whole exon sequencing transcript data in an embodiment of the present application. DETAILED DESCRIPTION

[0020] In order for those skilled in the art to better understand the technical solutions of the present application, the present application will be described in detail through specific embodiments. However, it should be understood that the specific embodiments are provided only for better understanding of the present application, and they should not be understood as limiting the present application. In the description of the present application, it should be understood that the terms used are only for the purpose of description, and cannot be understood as indicating or implying relative importance.

[0021] In order to solve the problem of more false positives in structural variation detection in three-generation whole transcriptome sequencing transcript data in the prior art, the present application provides a structural variation detection method, system and readable medium in three-generation whole exon sequencing transcript data, which comprises the following steps: performing three-generation whole transcriptome sequencing on a sample to obtain a whole transcriptome data set; performing TAGET mapping and annotation on the whole transcriptome data set to obtain a mapping result file and an annotation result file; obtaining transcripts that are not completely matched with the reference sequence according to the annotation result file as transcripts to be detected for structural variation; finding structural variation of the transcripts according to different mapping result files respectively; and reporting the final structural variation according to the screening standard of the structural variation. The present application can sensitively and accurately detect structural variation of transcripts, and reduce the false positive rate or the omission rate. The present application has great application value. The present application will be described below in conjunction with the drawings through embodiments.

[0022] Embodiment one

[0023] The present embodiment discloses a structural variation detection method in three-generation whole exon sequencing transcript data, as shown in Figure 1 The method comprises the following steps:

[0024] S1, a set of transcripts to be searched for structural variation is established.

[0025] The method for establishing the set of transcripts to be searched for structural variation comprises the following steps: performing three-generation whole transcriptome sequencing on a sample to generate three-generation whole transcriptome sequencing results; mapping the three-generation whole transcriptome sequencing results using TAGET software to obtain three-generation whole transcriptome sequencing annotation information and transcript information; and according to the annotation information, retaining transcripts that cannot be completely matched with the reference sequence, removing transcripts marked as ISM and FSM, and generating a set of transcripts to be searched for structural variation.

[0026] S2, according to the transcript information obtained by the TAGET software mapping, the set of transcripts is read in a loop to obtain the first structural variation of all transcripts.

[0027] S2.1 A method for obtaining a first structural variation or a second structural variation from transcript information, comprising the following steps:

[0028] S2.1.1 According to the gene annotation information of the transcript, the transcript to be searched for structural variation is matched with the reference transcript with annotated genes one by one, and if a certain reference transcript is highly similar to the transcript to be searched for structural variation at the breakpoint and does not have structural variation characteristics, it is considered that the transcript to be searched for structural variation does not have structural variation.

[0029] The structural variation includes duplication, inversion and deletion, and the deletion includes intron deletion and exon deletion.

[0030] S2.1.2 Otherwise, all ambiguous matching reference transcripts are retained, and a reference transcript set is generated.

[0031] S2.1.3 The transcript to be searched for structural variation and the reference transcripts in the reference transcript set are matched one by one, and whether the transcript to be searched for structural variation has structural variation is determined in order.

[0032] A method for determining whether a transcript to be searched for structural variation has structural variation, comprising the following steps:

[0033] S2.1.3.1 According to the transcript to be searched for structural variation, breakpoint information is obtained, the breakpoint information is matched with the breakpoint information of the reference transcript, information that the exons contained in the transcript to be searched for structural variation are mapped to the exon positions of the reference transcript is obtained, and whether multiple exons in the transcript to be searched for structural variation are mapped to the same exon in the reference transcript is determined.

[0034] S2.1.3.2 If there is, add the exon to the first exon set and record the mapped reference position, and determine whether the exons in the first exon set have three types of structural variations of duplication, inversion and deletion;

[0035] Determining whether the exons in the first exon set have three types of structural variations of duplication, inversion and deletion, comprising the following steps:

[0036] S2.1.3.2.1 Determine whether the exons in the first exon set have duplication structural variation, if there is, record the duplication structural variation and the breakpoint difference and the start and end points of the structural variation of the corresponding reference transcript;

[0037] S2.1.3.2.2 Remove the exons determined to have duplication structural variation, and generate a second exon set;

[0038] S2.1.3.2.3 If the second exon set is not empty, determine whether the exons in the second exon set have a deletion structural variation, and if so, record the deletion structural variation and its corresponding reference transcript breakpoint difference and structural variation start and end point;

[0039] S2.1.3.2.4 According to the positive and negative strand information in the annotation information, determine whether the transcript to be searched for a structural variation has an inversion structural variation, and record the inversion structural variation and its corresponding reference transcript breakpoint difference and structural variation start and end point;

[0040] S2.1.3.2.5 According to the information that the exons contained in the transcript to be searched for a structural variation are mapped to the exon positions on the reference transcript, determine whether the transcript to be searched for a structural variation has a whole exon deletion in the breakpoint information.

[0041] S2.1.3.3 If not, directly determine whether the transcript to be searched for a structural variation has an inversion structural variation according to the positive and negative strand information in the annotation information, and if so, record the inversion structural variation and its corresponding reference transcript breakpoint difference and structural variation start and end point;

[0042] S2.1.3.4 According to the information that the exons contained in the transcript to be searched for a structural variation are mapped to the exon positions on the reference transcript, determine whether the transcript to be searched for a structural variation has a whole exon deletion in the breakpoint information.

[0043] The method for determining whether the transcript to be searched for a structural variation has a whole exon deletion in the breakpoint information is:

[0044] S2.1.3.4.1 The exon in the reference transcript to which the first exon in the transcript to be searched for a structural variation is mapped is recorded as the first exon;

[0045] S2.1.3.4.2 The exon in the reference transcript to which the last exon in the transcript to be searched for a structural variation is mapped is recorded as the second exon;

[0046] S2.1.3.4.3 Determine whether there is an exon deletion between the first exon and the second exon.

[0047] S2.1.4 Screen the structural variations of each transcript, and retain the structural variations closer to the reference transcript and the unique reference transcript.

[0048] S3 According to the transcript information obtained by mapping with Hisat2 software, read the transcript set in a loop to obtain the second structural variation of all transcripts.

[0049] S4 filtering and screening the first structural variation and the second structural variation respectively to generate screened transcripts of the first structural variation and the second structural variation.

[0050] The method for filtering and screening the first structural variation and the second structural variation respectively:

[0051] Firstly, the same transcript cannot have structural variations mapped to different reference transcripts;

[0052] Secondly, the exon breakpoint set in the transcript without structural variations is the same as or similar to the corresponding exon breakpoint set on the mapped reference transcript, and structural variations with large breakpoint differences are not collected;

[0053] Thirdly, the deletion structural variation of the transcript must have a reference transcript meeting the standard in the second step;

[0054] Fourthly, the repeat and inversion structural variations of the transcript are recorded if there is no reference transcript meeting the standard in the second step, there is a deletion, and there is a repeat and inversion structural variation, and the non-actual transcript structural variation generated by mapping is reduced, mainly the deletion structural variation.

[0055] S5 combines the screened transcripts of the first structural variation and the second structural variation to obtain the final structural variation of the transcript.

[0056] Example Two

[0057] Based on the same inventive concept, the method established in Example One is used to detect the structural variations of the transcripts in the simulated data set in this embodiment to prove the effectiveness of the structural variation detection method in the present application. The specific steps are as follows:

[0058] According to the human reference sequence file (hg38) and the reference transcript information file, five groups of full-length transcriptome fasta data sets containing structural variations are simulated, wherein data sets 1-4 simulate that all transcripts only have one type of structural variation and only one exon in the same transcript has a structural variation, and data set 5 does not limit the type of structural variation and does not limit the number of exons in the same transcript with structural variations.

[0059] The TAGET software is used to map and annotate the five groups of full-length transcriptome fasta data sets respectively to obtain annotation information and transcript information.

[0060] The method established in Example 1 is used to detect the structural variations of the annotation information and transcript information of the five groups of full-length transcriptome fasta data sets respectively, and finally the structural variation results of the five groups of full-length transcriptome fasta data sets are obtained, as shown in Table 1.

[0061] Subsequently, the accuracy of the method in Example 1 was calculated by statistics on five groups of full-length transcriptome fasta data sets separately. The statistical results of the structural variation accuracy of data sets 1-4 are shown in Table 2, and the statistical results of the structural variation accuracy of data set 5 are shown in Table 3.

[0062] According to the structural variation accuracy statistics table of Table 2 and Table 3, the method in Example 1 can more accurately detect the structural variation of the third-generation full-length transcriptome data, and has the advantages of high precision, low false positive, and can more accurately find the case of exon whole deletion (DEL_whole) in the transcript.

[0063] Table 1 Structural variation results of five groups of full-length transcriptome fasta data sets

[0064]

[0065] Wherein, Transcript is the transcript number, Gene is the reference gene; Chr is the chromosome; Ref is the reference transcript; Sv is the structural variation type; Ref_exon_num is the sequence number of the exon in the reference transcript mapped by the structural variation; Start_site is the start position of the structural variation fragment on the reference sequence; End_site is the end position of the structural variation fragment on the reference sequence.

[0066] Table 2 Statistical results of structural variation accuracy of data sets 1-4

[0067]

[0068] Wherein, Type is the structural variation type; Known is the number of transcripts containing structural variation in the simulation data; Annotated is the number of transcripts in which the reference gene and the annotated reference gene of the TAGET mapping are consistent in the simulation data containing structural variation transcripts; Find sv is the number of transcripts containing the corresponding structural variation type detected by the structural variation detection method; Find sv (True) is the number of transcripts containing the corresponding structural variation type detected by the structural variation detection method, which is indeed simulated in the simulation data process; ratio(known) is equal to Find sv(True) / Known; ratio(Annotated) is equal to Find sv(True) / Annotated; Find ALL sv is the number of all transcripts containing structural variation detected by the structural variation detection method.

[0069] Table 3 Statistical results of structural variation accuracy of data set 5

[0070]

[0071] Embodiment three

[0072] Based on the same inventive concept, the embodiment discloses a system for detecting structural variations in transcript data of third-generation full-length transcriptome sequencing, comprising:

[0073] A transcript set establishing module is configured to establish a transcript set for which structural variations are to be found.

[0074] A first structural variation obtaining module is configured to obtain transcript information according to TAGET software mapping, and to cyclically read the transcript set to obtain first structural variations of all transcripts.

[0075] A second structural variation obtaining module is configured to obtain transcript information according to Hisat2 software mapping, and to cyclically read the transcript set to obtain second structural variations of all transcripts.

[0076] A screening module is configured to filter and screen the first structural variations and the second structural variations respectively, to generate screened transcripts of the first structural variations and the second structural variations.

[0077] An output module is configured to comprehensively output the screened transcripts of the first structural variations and the second structural variations, to obtain final structural variation conditions of the transcripts.

[0078] Embodiment four

[0079] Based on the same inventive concept, the embodiment discloses a computer readable storage medium, and the computer readable storage medium stores a computer program. The computer program is executed by a processor to implement the structural variation detection method in transcript data of third-generation whole exome sequencing according to any one of the above embodiments.

[0080] Based on the same inventive concept, the embodiment discloses a computer readable storage medium, and the computer readable storage medium stores a computer program. The computer program is executed by a processor to implement the gene data generation method based on a generative adversarial network according to any one of the above embodiments.

[0081] Those skilled in the art should understand that the embodiments of the present application can be provided as a method, a system, or a computer program product. Therefore, the present application can be in the form of a complete hardware embodiment, a complete software embodiment, or an embodiment combining software and hardware aspects. Moreover, the present application can be in the form of a computer program product implemented on one or more computer usable storage media (including but not limited to disk storage, CD-ROM, optical storage, etc.) containing computer usable program code.

[0082] The computer program instructions can also be loaded onto a computer or other programmable data processing apparatus to cause a series of operational steps to be performed on the computer or other programmable apparatus to produce a computer-implemented process such that the instructions which execute on the computer or other programmable apparatus provide steps for implementing the functions specified in the flowchart block or blocks. Figure 1 one or more flow or blocks. Figure 1 one or more flow or blocks.

[0083] These computer program instructions can also be stored in a computer-readable memory that can direct a computer or other programmable data processing apparatus to function in a particular manner, such that the instructions stored in the computer-readable memory produce an article of manufacture including instructions which implement the function specified in the flowchart block or blocks. Figure 1 one or more flow or blocks. Figure 1 one or more flow or blocks.

[0084] The computer program instructions can also be loaded onto a computer or other programmable data processing apparatus to cause a series of operational steps to be performed on the computer or other programmable apparatus to produce a computer-implemented process such that the instructions which execute on the computer or other programmable apparatus provide steps for implementing the functions specified in the flowchart block or blocks. Figure 1 one or more flow or blocks. Figure 1 one or more flow or blocks.

[0085] Finally, it should be noted that the above embodiments are merely intended to illustrate the technical solutions of the present application, rather than limit the same. Even though the present application has been described in detail with reference to the above embodiments, those skilled in the art should understand that the specific implementation manners of the present application can be modified or replaced equivalently without departing from the spirit and scope of the present application, and any modification or replacement without departing from the spirit and scope of the present application should be included in the protection scope of the present application. The above content is merely a specific implementation manner of the present application, but the protection scope of the present application is not limited to this. Any person skilled in the art can easily think of changes or replacements within the technical scope disclosed by the present application, and all the changes or replacements should be included in the protection scope of the present application. Therefore, the protection scope of the present application should be subject to the protection scope of the claims.

Claims

1. A method for detecting structural variations in third-generation whole-exome sequencing transcript data, characterized in that, The method comprises the following steps: establishing a transcript set to be searched for structural variation; mapping transcript information according to TAGET software, and cyclically reading the transcript set to obtain first structural variation of all transcripts; mapping transcript information according to Hisat2 software, and cyclically reading the transcript set to obtain second structural variation of all transcripts; respectively filtering and screening the first structural variation and the second structural variation to generate screened transcripts of the first structural variation and the second structural variation; comprehensively screening the screened transcripts of the first structural variation and the second structural variation to obtain final structural variation of the transcripts; The method for establishing the transcript set to be searched for structural variation comprises the following steps: performing third-generation full-length transcriptome sequencing on the sample to generate third-generation full-length transcriptome sequencing results; mapping the third-generation full-length transcriptome sequencing results by using TAGET software to obtain third-generation full-length transcriptome sequencing annotation information and transcript information; according to the annotation information, retaining transcripts that cannot be completely matched with reference sequences to generate a transcript set to be searched for structural variation.

2. The method for detecting structural variation in third-generation full-exon sequencing transcript data according to claim 1, wherein the method for obtaining first structural variation or second structural variation from transcript information comprises the following steps: according to gene annotation information of the transcripts, matching the transcripts to be searched for structural variation with reference transcripts of annotated genes one by one, if a certain reference transcript is highly similar to the transcript to be searched for structural variation at a breakpoint and does not have structural variation characteristics, it is considered that the transcript to be searched for structural variation does not have structural variation; otherwise, all ambiguous matching reference transcripts are retained, and a reference transcript set is generated; matching the transcripts to be searched for structural variation with reference transcripts in the reference transcript set one by one, and judging whether the transcripts to be searched for structural variation have structural variation in order; screening the structural variation of each transcript, and retaining structural variation closer to the reference transcripts and unique reference transcripts. The structural variation includes duplication, inversion and deletion, and the deletion includes intronic deletion and exonic deletion.

3. The method of structural variant calling in third generation whole exome sequencing transcript data of claim 2, wherein, The method for judging whether the transcripts to be searched for structural variation have structural variation comprises the following steps:

4. The method of structural variant calling in third generation whole exome sequencing transcript data of claim 3, wherein, ​ According to the breakpoint information of the transcript to be searched for structural variation, the breakpoint information is matched with the breakpoint information of the reference transcript to obtain information of the exons contained in the transcript to be searched for structural variation mapping to the exon positions of the reference transcript, it is judged whether there are multiple exons in the exons contained in the transcript to be searched for structural variation mapping to the same exon in the reference transcript, if there are, the exons are added to a first exon set, and the mapping reference positions are recorded, it is judged whether there are three types of structural variations of repetition, inversion and deletion in the exons in the first exon set, if not, it is directly judged according to the positive and negative strand information in the annotation information whether the transcript to be searched for structural variation has inversion structural variation, if yes, the inversion structural variation and the breakpoint difference and structural variation start and end points of the corresponding reference transcript are recorded; According to the information of the exons contained in the transcript to be searched for structural variation mapping to the exon positions of the reference transcript, it is judged whether there is a whole exon deletion in the breakpoint information obtained by the transcript to be searched for structural variation.

5. The method of structural variant calling in third generation whole exome sequencing transcript data of claim 4, wherein, The judgment of whether there are three types of structural variations of repetition, inversion and deletion in the exons in the first exon set comprises the following steps: It is judged whether the exons in the first exon set have repetition structural variation, if yes, the repetition structural variation and the breakpoint difference and structural variation start and end points of the corresponding reference transcript are recorded; The exons judged to have repetition structural variation are removed, and a second exon set is generated; If the second exon set is not empty, it is judged whether there is deletion structural variation in the exons in the second exon set, if yes, the deletion structural variation and the breakpoint difference and structural variation start and end points of the corresponding reference transcript are recorded; According to the positive and negative strand information in the annotation information, it is judged whether the transcript to be searched for structural variation has inversion structural variation, and the inversion structural variation and the breakpoint difference and structural variation start and end points of the corresponding reference transcript are recorded; According to the information of the exons contained in the transcript to be searched for structural variation mapping to the exon positions of the reference transcript, it is judged whether there is a whole exon deletion in the breakpoint information obtained by the transcript to be searched for structural variation.

6. The method for detecting structural variation in the transcript data of the third-generation whole-exome sequencing according to claim 5, wherein The method for judging whether there is a whole exon deletion in the breakpoint information obtained by the transcript to be searched for structural variation is as follows: The exon in the reference transcript to which the first exon in the transcript to be searched for structural variation maps is recorded as a first exon; The exon in the reference transcript to which the last exon in the transcript to be searched for structural variation maps is recorded as a second exon; It is judged whether there is an exon deletion in the exon region between the first exon and the second exon.

7. The method of structural variant calling in third generation whole exome sequencing transcript data of claim 6, wherein, The method for respectively filtering and screening the first structural variation and the second structural variation is as follows: Step 1: The same transcript cannot have structural variations mapping to different reference transcripts; Second step, the transcript does not contain the exon breakpoint set of structural variation, the corresponding exon breakpoint set of the mapped reference transcript is the same or similar, and the breakpoint difference is large. Structural variation is not included; Third step, the deletion structural variation of the transcript must have a reference transcript that meets the second step standard; Fourth step, if there is no reference transcript that meets the second step standard for the repeat and inversion structural variation of the transcript, and the repeat and inversion structural variation indeed exists, the reference gene is recorded; reduce the non-existent transcript structural variation generated by mapping.

8. A system for structural variant detection in third generation full-length transcriptome sequencing data, characterized in that, Comprise: The transcript set establishing module is used for establishing a transcript set to be searched for structural variation; The first structural variation obtaining module is used for obtaining transcript information according to TAGET software mapping, and the first structural variation of all transcripts is obtained by circulating reading the transcript set; The second structural variation obtaining module is used for obtaining transcript information according to Hisat2 software mapping, and the second structural variation of all transcripts is obtained by circulating reading the transcript set; The screening module is used for filtering and screening the first structural variation and the second structural variation respectively, and generating screened transcripts of the first structural variation and the second structural variation; The output module is used for comprehensively screening the transcripts of the first structural variation and the second structural variation, and obtaining the final structural variation of the transcript; The method for establishing the transcript set to be searched for structural variation comprises the following steps: Performing three-generation full-length transcriptome sequencing on the sample to generate three-generation full-length transcriptome sequencing results; Mapping the three-generation full-length transcriptome sequencing results by using TAGET software to obtain three-generation full-length transcriptome sequencing annotation information and transcript information; According to the annotation information, the transcripts that cannot be completely matched with the reference sequence are retained to generate the transcript set to be searched for structural variation.

9. A computer-readable storage medium, characterized in that, The computer readable storage medium stores a computer program, and the computer program is executed by the processor to realize the structural variation detection method in the three-generation full-exon sequencing transcript data according to any one of claims 1-7.

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