CN108256291A - It is a kind of to generate the method with higher confidence level detection in Gene Mutation result - Google Patents
It is a kind of to generate the method with higher confidence level detection in Gene Mutation result Download PDFInfo
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Abstract
The invention discloses a kind of methods for having higher confidence level detection in Gene Mutation result using having the generation of detection in Gene Mutation analysis result, the site mutation data file for the VCF forms that this method is generated using gene mutation analysis software, statistics is in each file, the genotype and its distribution situation of quality information recorded in variant sites removes the site of low genotype quality.And the mutational site data file of comprehensive two kinds of Software Creates, it extracts in the site for having identical variation with a position, generation relatively has the gene mutation data file that detection in Gene Mutation analysis result has higher confidence level, for subsequent analysis flow.
Description
Technical field
The present invention relates to biological gene mutation analysis fields, are analyzed more particularly to a kind of using existing detection in Gene Mutation
As a result method of the generation with higher confidence level detection in Gene Mutation result.
Background technology
Genome sequencing is by the way that with the high-throughput gene sequencing technology of a new generation, high power is carried out to personal full-length genome
The sequencing of rate, then result and standard human's genome are compared, obtain the process of complete personal whole genome sequence.Closely
Over a little years, by extensive epidemiological survey, scientists have been found that a large amount of genetic mutation and the close phase of human diseases
It closes.
With the rapid development of high throughput sequencing technologies, using newest large-scale gene sequencer and cost significantly
Decline, full genome detection has been able to detect most hereditary information in genes of individuals group.But how to so huge
Sequencing sequence analyzed and handled, exactly stubborn problem the most now.Therefore, a large amount of gene data analysis software
It comes into being.
The data analysis flow of full-length genome mainly includes quality control, sequence alignment, abrupt climatic change, mutation annotation.Mesh
Preceding application is the most universal the analysis of biological information software such as GATK, Atlas, BWA, Samtools.Wherein, gene comparison software
BWA is mainly used for carrying out sequence alignment from the initial data of sequencing, and the comparison data of generation is usually deposited with SAM file formats
Storage.Gene mutation analysis software Samtools can be converted into SAM files binary BAM files, substantially reduce required
Memory space, and improve the efficiency of data analysis.Therefore BAM files are that most widely used sequencing data stores lattice at present
Formula.By aforesaid operations, a human genome with standard gene group is compared, finds out various gene mutations, including SNPs,
The several genes mutation analysis software such as Indels is adapted to, most widely used gene mutation analysis software include GATK,
Atlas and Samtools.
The standards of grading and algorithm that each analysis software has its exclusive, then determine each according to these standards of grading
Site is with the presence or absence of mutation.However pass through practice for many years, it has been found that all there are many deficiencies for each points-scoring system, cause to dash forward
The recall rate and false positive of change are all excessively high, largely affect the development of subsequent experimental.
The standards of grading and algorithm that each gene mutation analysis software has its exclusive, then determine according to these standards of grading
With the presence or absence of mutation, the testing result of a site mutation is that there are results for the maximum probability based on statistics in each fixed site.
No matter which kind of algorithm, as long as the number of repetition of segment is more in initial data, around the site and reference gene group compares one
Cause property is higher, and " support " which obtains is stronger, and credible result degree is higher.Confidence level is recorded in each prominent
Become in the GQ labels in the Format row in site, referred to as genotype quality (Genotype Quality), be defined as GQ=-10*
Log (1-p), p are probability existing for genotype, it is seen that GQ values are bigger, and the possibility of the site sequencing result is bigger.
By " high probability " principle of gene mutation analysis software it is found that in the detection knot to same gene detection different software
In fruit, such as occur identical variation testing result in same site, illustrate this site in different software, all with high probability branch
It holds this site and produces variation.I.e. in different genes mutation analysis software, such as certain variation is all detected in same position, that should
The confidence level that this variation has occurred in position is higher.Therefore even if different genes mutation detecting analysis software is to same analysis pair
In the testing result of elephant, it even if respectively the Mass Distribution of different genotype is different, can also merge, generate relatively existing inspection
Survey the genetic test mutation result as a result, with higher confidence level
Invention content
According to above-mentioned technical background, the present invention uses following technical proposals：
S1, analysis gene initial data is pre-processed, obtains cdna sample data；
S2, using arbitrary two kinds of gene mutation analysis software, the cdna sample data are analyzed respectively, are obtained
The mutational site detection data of VCF file formats；
S3, change point bit distribution statistics is carried out respectively to two kinds of Software Create VCF files, according to respective site GT values and GQ
Distribution value situation determines GQ threshold values, and screens variant sites in original VCF files, each self-generating according to threshold value in certain proportion
VCF files to be combined；
S4, processing is merged to the consistent site in the VCF files to be combined, generates and have detection in Gene Mutation point
Analysing result generation has compared with high gene type quality detection in Gene Mutation result data files；Higher confidence level is defined as opposite S2 and walks
The mutational site detection data confidence level higher generated in rapid；
Preferably, the step S1 includes：
S11, it is analysed to gene initial data and standard gene group is compared, determines the position of short sequence in the genome
It puts, and by short sequence assembling into complete reference gene group data；
S12, it resequences to the reference gene group data according to predetermined order, obtains the reference gene group number
According to binary format file；
S13, it adds sequence head accordingly on the binary format file of the reference gene group data, obtains binary system
The cdna sample data of form；
Preferably, the step S1 further comprises：
S14, part is carried out to the gene data of the binary format, and comparison and sequencing quality recalculate again, obtain
The cdna sample data of sequencing quality optimization.
Preferably, the step S2 includes：
S2, with two kinds of detection in Gene Mutation softwares respectively by sequencing quality optimize cdna sample data and standard gene group
It is compared, finds out various gene mutation information, change information and small fragment insertion/deletion etc. including site, each self-generating is treated
Optimize VCF files.
Preferably, the step S3 includes：
S31, using the combination of VCF files CHROM and POS to be optimized as index, to each VCF files carry out
The progressive scan of valid data row；
S32, in S31 scanning processes, read the GT values being present in each variant sites in Format row and GQ values, and unite
For meter in each VCF files, different GT values correspond to GQ Distribution values situation in variant sites.Count different GT values corresponding sites simultaneously
Total quantity；
S33, different GT values GQ Distribution value situations are counted according to S32 steps, calculates difference GT values site pair in the VCF files
The GQ threshold values answered；
S34, again using the combination of CHROM and POS as index, it is corresponding to each detection in Gene Mutation software
VCF files carry out the progressive scan extraction GT and GQ values of valid data row respectively, when the GT that GQ values are more than S33 step calculating corresponds to threshold
During value, the row site information is exported to a new VCF files.VCF files to be combined are generated after the end of scan；
Preferably, GT values described in S3 steps correspond to threshold value satisfaction, and in GT value corresponding sites, GQ values are less than the site of threshold value
Quantity is a designated ratio of site total quantity；
Preferably, the step S4 includes：
S41, the VCF files to be combined to generation, respectively using the combination of CHROM and POS as index be index into
Row progressive scan；
S42, in scanning process, such as in two files, same corresponding respective ALT of index is equal, by two files
CHROM, POS, REF, ALT, GT, GQ and other information needed are combined by VCF file format rows, and are output to a new VCF
In file.To the end of scan, this VCF file is exactly to generate with higher confidence level detection in Gene Mutation result data files.
Higher confidence level is defined as the mutational site detection data confidence level higher generated in opposite S2 steps.
Beneficial effects of the present invention are as follows：
Original sample will be sequenced from same gene in technical solution of the present invention, with two kinds of different genes abrupt climatic changes
The mutational site data file of the VCF forms of Software Create corresponds to variant sites by calculating each VCF files difference GT values
GQ is distributed, and screening removes the site of low GQ values, and the variant sites information after screening is merged, and generation has higher credible
The accidental data file of degree is laid a solid foundation for follow-up study exploitation.
Description of the drawings
The specific embodiment of the present invention is described in further detail below in conjunction with the accompanying drawings；
Fig. 1 shows typical VCF formatted files；
Fig. 2 shows removal low quality gene mutation site algorithm flow charts；
Fig. 3 shows the algorithm flow chart for merging the site of two kinds of gene mutation Software Creates；
Fig. 4 shows overall flow figure.
Specific embodiment
In order to illustrate more clearly of the present invention, the present invention is done further with reference to preferred embodiments and drawings
It is bright.Similar component is indicated with identical reference numeral in attached drawing.It will be appreciated by those skilled in the art that institute is specific below
The content of description is illustrative and be not restrictive, and should not be limited the scope of the invention with this.
The invention discloses a kind of gene point mutation data files using two kinds of Software Creates, optimize, combine
To generate the method for confidence level detection in Gene Mutation data file.Concrete scheme of the present invention is as follows：
First, using several genes mutation analysis software, gene initial data to be analyzed is pre-processed, generates gene
Sample data, specifically：
It is analysed to gene initial data and standard gene group and carries out comparison to be compared with standard gene group, determine short sequence
Row position in the genome, and by short sequence assembling into complete reference gene group data, short sequence assembling into complete
Mankind's reference gene group file；It resequences to the reference gene group data according to predetermined order, obtains the reference
The binary format file of genomic data；Sequence is added accordingly on the binary format file of the reference gene group data
Row head obtains the cdna sample data of binary format；Part is carried out to the gene data of the binary format to compare again
It is recalculated with sequencing quality, obtains the cdna sample data of sequencing quality optimization.
Second step using two kinds of detection in Gene Mutation softwares, obtains the variation message file of VCF forms, specifically：
With the cdna sample data of the quality optimization, with two kinds of detection in Gene Mutation softwares and standard gene group respectively into
Row compares, and finds out various gene mutation information, and generation includes the orderly to be optimized of site change information and small fragment insertion/deletion
VCF files.
Generation mutational site file is VCF forms after gene mutation analysis detection, and what this form divided by " # " symbol started says
Outside bright information row, valid data information row is by CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT etc. 10
Row and several self-defined row compositions, wherein CHROM are classified as chromosome, and POS is classified as position, and REF is reference nucleotide, and ALT is
Variant nucleotides have recorded GT information and GQ information in FORMAT row, the genotype (Genotype) that respectively currently makes a variation and
The mass value (Genotype Quality) of genotype, GQ values are represented in possibility existing for the genotype of the site.The value is got over
Height, then the confidence level of testing result is bigger.Typical VCF formatted files are shown in Fig. 1.
Third walks, by the orderly VCF files of generation, according to the distribution that different GT and GQ is corresponded in respective site information,
Low GQ values site is removed, specifically：
Using the combination of VCF files CHROM and POS to be optimized as index, each VCF files are carried out respectively
The progressive scan of valid data row；The GT values in each row variation site and GQ values are read, and is counted in single VCF files, it is different
GT values correspond to GQ Distribution values situation in variant sites.The total quantity of different GT values corresponding sites is counted simultaneously；It is different according to statistics
GT value GQ Distribution value situations calculate the corresponding GQ threshold values in difference GT values site in the VCF files；VCF files are rescaned, are made
The GQ values for obtaining designated ratio are less than the site of the threshold value, are all deleted, and export high GQ sites, form high VCF texts to be combined
Part.Screening process is shown in Fig. 2.
VCF files to be combined are carried out the merging of identical entry, specifically by the 4th step：
By VCF files to be combined, progressively scanned respectively using the combination of CHROM and POS as index for index；
In scanning process, such as in two files, same corresponding respective ALT of index is equal, by CHROM, POS of two files,
REF, ALT, GT, GQ and other information needed are combined by VCF file format rows, and are output in a new VCF files.It closes
And flow is shown in Fig. 3.
Below by one group of embodiment, the present invention will be further described：
1st, from thousand human genome FTP (ftp：//ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/
Data it is the data file under HG00731 files that lower number is downloaded on), then is selected using similary process flow early period, right
Initial data to be analyzed obtained after genome alignment, genome rearrangement sequence, addition sequence head and sequencing quality recalculate
Quality optimization cdna sample data：HG00731.mapped.ILLUMINA.bwa.PUR.low_
coverage.20130422.bam。
2nd, with the cdna sample data of the quality optimization, using human_g1k_v37.fasta as reference gene group, difference
With Samtools and Gatk programs, everyone various gene mutation information are found out, generation includes site and changes information and small pieces
Section is inserted into or the orderly VCF files of missing, software command form are respectively."samtools mpileup--skip-indels-
Uf% (reference) s% (local_dir) s/% (bam) s | bcftools call--skip-variants indels-
Mv-Ov-f GQ-o% (local_dir) s/% (vcf) s " and " java-Xmx2g-jar/mnt/bioinfo/GATK/
GenomeAnalysisTK.jar-T HaplotypeCaller-R% (reference) s--annotation
QualByDepth--annotation HaplotypeScore--annotation
MappingQualityRankSumTest--annotation ReadPosRankSumTest--annotation
FisherStrand--annotation AlleleBalance--annotationRMSMappingQuality-l INFO-
Stand_call_conf 50-stand_emit_conf 10-dcov 1000-I% (local_dir) s/% (bam) s-o%
(local_dir) s/% (vcf) s-nct 2 ".Samtools.hg00731.vcf and gatk.hg00731.vcf texts are generated respectively
Part
3rd, by the VCF files to be optimized --- samtools.hg00731.vcf and gatk.hg00731.vcf files
The combination of CHROM and POS carries out each VCF files the progressive scan of valid data row as index；
In scanning process, the GT values being present in each variant sites in Format row and GQ values are read, and count each
In VCF files, different GT values correspond to GQ Distribution values situation in variant sites.The sum of different GT values corresponding sites is counted simultaneously
Amount；As a result such as table 1.
According to different GT values GQ Distribution value situations are come out, in the case where specified screening ratio is 0.01, calculate
The corresponding GQ threshold values in difference GT values site in the VCF files；As a result such as table 2.
Again using the combination of CHROM and POS as indexing, to samtools.hg00731.vcf with
Gatk.hg00731.vcf files progressive scan extraction GT and GQ values, when the GT that GQ values are more than the calculating of table 2 corresponds to threshold value, output
The row site information is to a new VCF files.VCF files to be combined are generated after the end of scan:
Filter.samtools.hg00731.vcf and filter.gatk.hg00731.vcf
4th, to filter.samtools.hg00731.vcf and filter.gatk.hg00731.vcf, respectively with CHROM
Item and the combination of POS are progressively scanned as index to index；In scanning process, such as in two files, same index
Corresponding respective ALT equal, by CHROM, POS, REF, ALT, GT, GQ of two files and other information needed, by VCF files
Format string is combined, and is output to a new VCF files merge.hg00731.vcf.To the end of scan,
Merge.hg00731.vcf files are exactly to generate with higher confidence level detection in Gene Mutation result.
Obviously, the above embodiment of the present invention be only to clearly illustrate example of the present invention, and not be pair
The restriction of embodiments of the present invention for those of ordinary skill in the art, may be used also on the basis of the above description
To make other variations or changes in different ways, all embodiments can not be exhaustive here, it is every to belong to this hair
The obvious changes or variations that bright technical solution is extended out are still in the row of protection scope of the present invention.
Claims (7)
1. a kind of side that there is higher confidence level detection in Gene Mutation result using having the generation of detection in Gene Mutation analysis result
Method, which is characterized in that the step of this method includes：
S1, analysis gene initial data is pre-processed, obtains cdna sample data；
S2, using arbitrary two kinds of gene mutation analysis software, the cdna sample data are analyzed respectively, obtain VCF texts
The mutational site detection data of part form；
S3, change point bit distribution statistics is carried out respectively to two kinds of Software Create VCF files, according to respective site GT values and GQ values point
Cloth situation determines GQ threshold values, and screens variant sites in original VCF files according to threshold value in certain proportion, and each self-generating is waited to close
And VCF files；
S4, processing is merged to the consistent site in the VCF files to be combined, generates and have detection in Gene Mutation analysis knot
Fruit generation has higher confidence level detection in Gene Mutation result data files；Higher confidence level is defined as generating in opposite S2 steps
Mutational site detection data confidence level higher.
2. a kind of generated using existing detection in Gene Mutation analysis result according to claim 1 has higher confidence level base
Because of the method for abrupt climatic change result, which is characterized in that the step S1 includes：
S11, it is analysed to gene initial data and standard gene group is compared, determines the position of short sequence in the genome,
And by short sequence assembling into complete reference gene group data；
S12, it resequences to the reference gene group data according to predetermined order, obtains the reference gene group data
Binary format file；
S13, it adds sequence head accordingly on the binary format file of the reference gene group data, obtains binary format
Cdna sample data.
3. a kind of generated using existing detection in Gene Mutation analysis result according to claim 2 has higher confidence level base
Because of the method for abrupt climatic change result, which is characterized in that the step S1 further comprises：
S14, part is carried out to the gene data of the binary format, and comparison and sequencing quality recalculate again, are sequenced
The cdna sample data of quality optimization.
4. the method for evaluation detection in Gene Mutation analysis process error according to claim 1, which is characterized in that the step
Rapid S2 includes：
S2, cdna sample data and standard gene group that sequencing quality optimizes are carried out respectively with two kinds of detection in Gene Mutation softwares
It compares, finds out various gene mutation information, change information and small fragment insertion/deletion etc. including site, generate VCF texts to be optimized
Part.
5. a kind of generated using existing detection in Gene Mutation analysis result according to claim 1 has higher confidence level base
Because of the method for abrupt climatic change result, which is characterized in that the step S3 includes：
S31, using the combination of VCF files CHROM and POS to be optimized as index, each VCF files are carried out effective
The progressive scan of data row；
S32, in S31 scanning processes, read be present in each variant sites Format row in GT values and GQ values, and count exist
In each VCF files, different GT values correspond to GQ Distribution values situation in variant sites.Count the total of different GT values corresponding sites simultaneously
Quantity；
S33, different GT values GQ Distribution value situations are counted according to S32 steps, it is corresponding calculates difference GT values site in the VCF files
GQ threshold values；
S34, again using the combination of CHROM and POS as index, VCF corresponding to each detection in Gene Mutation software text
Part carries out the progressive scan extraction GT and GQ values of valid data row respectively, when the GT that GQ values are more than S33 step calculating corresponds to threshold value,
The row site information is exported to a new VCF files.VCF files to be combined are generated after the end of scan.
6. a kind of according to claim 5 have higher confidence level gene using existing detection in Gene Mutation analysis result generation
The method of abrupt climatic change result, which is characterized in that the GT values correspond to threshold value satisfaction, and in GT value corresponding sites, GQ values are less than
The bit number of points of threshold value are a designated ratio of site total quantity.
7. a kind of according to claim 1 have higher confidence level gene using existing detection in Gene Mutation analysis result generation
The method of abrupt climatic change result, which is characterized in that the step S4 includes：
S41, the VCF files to be combined to generation, respectively using the combination of CHROM and POS as index for index progress by
Row scanning；
S42, in scanning process, such as in two files, same corresponding respective ALT of index is equal, by two files
CHROM, POS, REF, ALT, GT, GQ and other information needed are combined by VCF file format rows, and are output to a new VCF
In file.To the end of scan, this VCF file is exactly to generate with higher confidence level detection in Gene Mutation result；It is higher credible
Degree is defined as the mutational site detection data confidence level higher generated in opposite S2 steps.
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Cited By (4)
| Publication number | Priority date | Publication date | Assignee | Title |
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| CN109346127A (en) * | 2018-08-09 | 2019-02-15 | 中山大学 | A kind of statistical analysis technique driving gene for detecting potential cancer |
| CN109920484A (en) * | 2019-02-14 | 2019-06-21 | 北京安智因生物技术有限公司 | A kind of analysis method and system of the genetic test data of sequenator |
| CN111899790A (en) * | 2020-08-17 | 2020-11-06 | 天津诺禾医学检验所有限公司 | Sequencing data processing method and device |
| TWI785847B (en) * | 2021-10-15 | 2022-12-01 | 國立陽明交通大學 | Data processing system for processing gene sequencing data |
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2016
- 2016-12-28 CN CN201611234002.2A patent/CN108256291A/en active Pending
Cited By (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN109346127A (en) * | 2018-08-09 | 2019-02-15 | 中山大学 | A kind of statistical analysis technique driving gene for detecting potential cancer |
| CN109346127B (en) * | 2018-08-09 | 2021-10-08 | 中山大学 | Statistical analysis method for detecting potential cancer driver gene |
| CN109920484A (en) * | 2019-02-14 | 2019-06-21 | 北京安智因生物技术有限公司 | A kind of analysis method and system of the genetic test data of sequenator |
| CN111899790A (en) * | 2020-08-17 | 2020-11-06 | 天津诺禾医学检验所有限公司 | Sequencing data processing method and device |
| TWI785847B (en) * | 2021-10-15 | 2022-12-01 | 國立陽明交通大學 | Data processing system for processing gene sequencing data |
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