lib BuildDatabase -name GDB -engine ncbi. Command-lines using BioProject accessions. db=hgcentral. The import function in the rtracklayer package (also used by makeTxDbFromGFF internally). gff3 transcripts. Background. dat file to gff3 . The GTF (General Transfer Format) is identical to GFF version 2. For more information, refer to the GFF3 specification. Gene reference names and coordinates were retrieved from the GENCODE project through the European Bioinformatics Institute FTP server. The Buell Lab at the University of Georgia is pleased to make available an updated long-read chromosome-scale genome assembly (v6. gt gff3validator my. GFF3 addresses this and other deficiencies. Zm-B73-REFERENCE-NAM-5. About Rgff. pl","contentType":"file. gff3:353322: HMEL021863g1. PepsiCo_OT3098_V2_panoat_nomenclature_annotation_release_doc. Open the maker_opts. In a GenBank file, sequences are broken into discrete parts which can be parsed as. We would like to show you a description here but the site won’t allow us. If the input to prokka was a multi-FASTA, then this will be a multi-Genbank, with one record for each sequence. 論文発表されたアノテーションファイル(gff3 (gtf)ファイル)の情報を基に、ゲノムfastaファイルから配列情報を抽出する。 ツール ・gffread. tuberosum Group Phureja DM 1-3 516 R44. The GFF3 format is a commonly-used one in bioinformatics for representing sequence annotation. Genome annotation files are provided in GFF3 format for all annotated assemblies included in NCBI’s Genomes FTP resource. sh script that you can execute to demonstrate. You can use lib/gff3_ID_generator. You can find the specification here:The easiest way is to use the gffread program that comes with the Cufflinks software suite (Tuxedo) gffread my. GTF is similar to GFF3 and is sometimes referred to as GFF2. Version 3 (GFF3) is the preferred version. makeTxDbFromUCSC and makeTxDbFromBiomart for convenient ways to make a TxDb object from UCSC or BioMart online resources. Share Improve this answer Genome annotation pipeline. You can also skip sortBed altogether, as gff2bed uses BEDOPS sort-bed internally: $ gff2bed < myfile. simple replacement – a model has a single replace tag. Predict functions of each gene Output files: Gene description (human. GTF. GFF3sort takes a GFF3 file as its input data and returns a sorted GFF3 file as output. Improve TE summary (*. Get started using our web pages and tools, learn common workflows and data requests for our web pages, command-line tools, python and R packages. Genome annotation files are provided in GFF3 format for all annotated assemblies included in NCBI’s Genomes FTP resource. 6. pl input. (2015). This function should be more efficient than using read. However, current tools available for GFF3 file sorting have some limitations and their sorting results would lead to erroneous rendering in JBrowse. NAME; SYNOPSIS; DESCRIPTION; GFF3 AND SEQUENCE DATA; TODO; FEEDBACK. 4_de_novo_gene_finders. Directly from this repository. For other annotation files, only the CRI assembly of Gossypium hirsutum is provided and. gff3 > 31_36. life404 commented on Apr 12, 2022. Converting a SNP GFF3 file to VCF format gff converter for use with mummer/promer (microbial genome) Annotating sequences for Gbrowse - which is the database and which is the query?The gffread utility can convert from gff to gtf quite nicely and is generally useful for other processing on gff files (extracting fast of genes, etc). This project aims to provide a straightforward end-to-end pipeline that takes as input a HAL-format multiple whole genome alignment as well as a GFF3 file representing annotations on one high quality assembly in the HAL alignment, and produces a output GFF3 annotation on all target genomes chosen. However, many databases are still not equipped to handle GFF3 version. We should merge all GFF files from all gene predictions into one file. To do that, GFF3 files can be loaded into programs like Web Apollo, GBrowse, and JBrowse. gff3. But for some species there is no available annotation in gff format in NCBI but only in gbff format. Use GTF over GFF3. gencode. 2. Usage: gb2gff [options] Files Options: -h, --help print help and exit --helpFormat What kind of help. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. Thanks for the detailed and helpful e-mail Leighton. 1使用augustus对基因组序列进行基因预测分析，保存GFF格式的预测结果。. gz. gff3 -g genome. py <GFF annotation file> <FASTA sequence file> """ import sys import. Run the braker with --gff3 parametrs. sum) by splitting overlapping TEs and force each bp annotated only once. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. This is still a work in progress and I'll hopefully be adding features soon. The gff3 file was created as output of GMAP, and contains the transcripts as found by alignment to the reference (specifying option -f gff3_match_cdna ). Gene predictions. 2. seqid：参考序列的id。. ends up giving me this error:Updating the GFF3 + Fasta to GeneBank code. However, the flexibility existing in the GFF3 format makes this conversion task difficult to perform. S. The gene annotation file is needed for creating the known splice junctions to improve the accuracy of the genome mapping. Represents nucleotide sequences, including metadata, annotation and the sequence itself. 5. gff3 transcripts. R01 HG006677/HG/NHGRI NIH HHS/United States. 2. We have developed the GFF3toolkit to help identify common problems with GFF3 files; fix 30 of these common problems; sort GFF3 files (which can aid in using down-stream processing programs and custom parsing); merge two GFF3 files into a single, non-redundant GFF3 file; and generate FASTA files from a GFF3 file for many use cases. Converting the GFF3 format to a format accepted by one of the three INSDC databases is a key step in the achievement of genome annotation projects. Select a file containing functional domain information with protein coordinates, formatted as four tab-delimited columns: “Gene ID,” “Start Pos,” “End Pos,” and “Name of Domain. All GFF tracks must be formatted according to Sanger's GFF2 specification. 15 (replaced) RefSeq assembly. password=password central. 1 assembly as provided by Animalgenome. The GFF3 format was developed to permit the exchange and comparison of gene annotations between different model organism databases . Specify the file name with the -g1 or –gff_file1 argument. 20200622, RefSeq Functional Element features are indicated by the 'RefSeqFE' source in column 2 of NCBI GFF3 files. Cupcake ToFU: supporting scripts for Iso Seq after clustering step. GFF3 addresses several shortcomings in its predecessor, GFF2. 从头预测，同源注释和转录组整合都会得到一个预测结果，相当于收集了大量证据，下一步就是通过这些证据定义出更加可靠的基因结构，这一步可以通过人工排查，也可以使用EVidenceModeler (EVM). cdna_alignment_orf_to_genome_orf. 1. P. Windows Mac Linux iPhone Android. fasta > best_candidates. I'll also forward to the MAKER list. , a single feature that exists over. eclipsed_orfs_removed. TEsorter是基于保守蛋白结构域以及 REXdb数据库进行分类。 TEsorter不仅仅可以对LTR-RTs进行分类，还可以对其它Class Ⅰ以及Class Ⅱ等类型的TE进行分类，只要 REXdb数据库覆盖了的TE都可以分类，具体如下：--mobile_element ¦--Class_I ¦ ¦--SINE ¦ ¦--LTR ¦ ¦ ¦--Ty1 ¦ ¦ ¦ °--copia ¦ ¦ ¦ ¦--Ale ¦ ¦ ¦ ¦--Alesia. 如何对基因组进行注释. Usage gtf_to_gff3(gtfFile, outFile, forceOverwrite = FALSE. It supports flexible integration of all the common types of genomic data and metadata, investigator-generated or publicly available, loaded from local or cloud sources. gz: a FASTA file containing the plant proteins released with SwissProt All of this data can also be. and it tells me it's valid. I want to get the annotations in gff format for a assembled genome. I don't know any simple method for what you ask, mainly because gff3 format does not contain sequences (only annotations) while fasta & genbank do. melanogaster genomes. The only one keeping comments at the beginning of the file. For windows users that have installed TBtools from an exe file, double click the TBtools icon and the main panel of TBtools will pop up. Specifying the GFF3 annotation file for the annotated complex repeats (rm_gff) has the effect of hard masking these repeats so that they do not confound our ability to identify coding genes. gff3 output. At the core of the prediction algorithm is Evidence Modeler, which takes several different gene prediction inputs and outputs consensus gene models. I'll have a look at this tonight and make the necessary corrections to the GFF3 spec. 3. type == 'CDS': print (feature) No output is returned whatsoever. hints. I don't know any simple method for what you ask, mainly because gff3 format does not contain sequences (only annotations) while fasta & genbank do. Yes (Only if the feature is present in the file. Optionally, Fasta sequences can be appended to the end of a GFF3 file (separated by a ##FASTA. The two versions are similar but are not compatible and scripts usually only work with one of. The NCBI Datasets Genome Data Package contains genome sequences and metadata for a set of requested assembled genomes. Per GenCode rule, stop_codon is not part of CDS but it is part of mRNA or exon. GFF3 addresses several shortcomings in its predecessor, GFF2. gbk: This is a standard Genbank file derived from the master . gff3') And people wonder why R is so popular for bioinformatics. Splitting rule. [ Link] OR NEWLY PUBLISHED COTTON GENOMES. The last update on 02-05-2018: the genome visualization browser function has been suspended until the related browser issue can be solved. gfftobed. Genes are in blue, the transcripts are the small red lines, non-coding. This file must be the Fasta file that the GFF3 seqids and coordinates refer to. $\endgroup$ – Add a comment. gtf-type file are then gathered to create an annotation file for. Support . gz) Annotation, Gene, Transcript 7. Click “Version” to check whether the current TBtools is the latest version. 1. gff3. Reccommend: use RATT first. As the title suggest, you will need your genome gff3 and fasta reference as inputs. GFF3格式文件为文本文件，分为9列，以TAB分开。. GFF3/GTF 4. Design Vision Updates to the Left Navigation. The basic characteristics of the file formats are described at: GFF3: GTF:. TxDb Objects. See this link for more information. Download. hints. You can view a sample GenBank record displayed in the GenBank Flat File format that includes definitions. /gff3_to_gtf_converter. Bo Hu, Jinpu Jin, An-Yuan Guo, He Zhang, Jingchu Luo and Ge Gao. Usage: gff_to_genbank. If the GFF3 files is successfully parse, it is converted to gene, annotation. Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files. Download FASTA files for genes, cDNAs,. This function should be more efficient than using read. py < mydata. For most genomes annota. config. Only needed to be used if your original GFF3 files have parent features appearing behind their children features. I made an input of gff. It is an incredibly flexible, 9-column format, which is easily manipulated by biologists. The Integrative Genomics Viewer (IGV) is a high-performance, easy-to-use, interactive tool for the visual exploration of genomic data. using bedtools) or load them into other graphical tools that support these file types. )5. The GFFFile class extends RTLFile and is a formal represention of a resource in the GFF format. Genome data packages can be downloaded by NCBI Taxonomy ID or taxonomic name, NCBI Assembly accession, or NCBI BioProject accession. Description Usage Arguments Details Value Author(s) See Also Examples. Update your old Ensembl IDs. Alignments. fq. Running this script will convert the sequence. 在最新版本的GFF文件中(GFF3)，有一些是已经预先定义的属性特征，并且这些特征往往还有特殊的含义：ID这个标签实在各行都要有的；另外有一个Parent的属性，它指明type所从属的上一级ID。 GTF. BED stands for Browser Extensible Data. CHAPTER 1 gff3_QC readme 1. , a single feature that exists over. tar_. py # ===== from gff3 import Gff3 # initialize a Gff3 object gff = Gff3 # parse GFF3 file and do syntax checking, this populates gff. The GenomicFeatures package uses TxDb objects to store transcript metadata. Currently, only gene features are reported for the BED and CSV formats. ctl, maker_exe. Then create the file data/tracks. Add a comment. gff3 can not be used. gff-rename. This flexibility has a drawback aspect, there is an incredible amount of. 如果未知，则用点. fasta_external gff. thaliana in the main SNAP directory. DNA methylation, transcription factor binding sites, histone modifications, and regulatory features such as enhancers and repressors, and microarray annotations. MAKER will not attempt to validate the features, but will just pass them through "as is" to the final GFF3 file. GTF GFF3. The GFF3 format is commonly used for the annotation of genomic coordinates and is a popular data exchange format, particularly within the Generic Model Organism Database (O’Connor et al. For example : braker. Predict functions of each gene Gene ID Gene description GRMZM2G002950 Putative leucine-rich. GFF2 (aka GTF) files can also be read: use GFF3 = FALSE to have the correct field names. It is especially convenient if your are working on large gff3 files. 50 errors converting GFF3 file:. sh script that you can execute to demonstrate the entire process, starting from a cufflinks GTF file. FASTA 2. ” This file can be prepared using CD-search (Marchler-Bauer et al. mamba create -n genbank_to genbank_to conda activate genbank_to genbank_to --help. gffread gene. gff3|less -S to get only intact LTRs. GFF-Ex is a genome feature based sequence extraction package to automate sequence extraction based on the features defined within feature files (Figure 1 ). [ Similarly to prepare your data for submission to NCBI please use Genome Annotation Generator -. gff3; kegg; or ask your own question. gff3. group_ORF_sequences. In my . What can I find? Protein-coding and non-coding genes, splice variants, cDNA and protein sequences, non-coding RNAs. 0. JBrowse. sort. intact. Liftoff. 如图所示，gff3文件主要有以#开始的行数，为基因注释行，起到注释信息的作用，没. GenBank format An example of a GenBank record may be viewed here. You can start by ensuring your list of target genes is sorted in the same order as the GFF file,. Let's see how that goes. Geneious also supports GFF3 and GTF formats. gt featureindex Retrieve annotations from a persistent feature index as GFF3 output. The data package may include genome, transcript and protein sequences in FASTA format, annotation in GFF3, GTF, and GBFF formats, data reports containing metadata in JSON Lines format, and a subset of. gff3 Optional Parameters: --precise Run in precise mode, about 2X~3X slower than the default mode. repeatmasker. As discussed here: miRTop/incubator#10 we've defined a GFF3 format for output of small RNA pipelines focused on miRNA data currently. 5. 1. Step 2: Build using gene annotations and reference sequences. The unmapped gene annotation can be found here (gtf, gff3) GTF GFF3: Basic gene annotation: CHR: It contains the basic gene annotation on the reference chromosomes only; This is a subset of the corresponding comprehensive annotation, including only those transcripts tagged as 'basic' in every gene; GTF GFF3: Long non-coding RNA gene. September 23, 2020 - The paper "Construction of a chromosome-scale long-read reference genome assembly for. However, before coveting, you need delete the ; at the end of lline of braker. In practice, sort-bed tool is faster than GNU sort and sortBed and is non-lossy *shrug*. GFF3 format A GFF3 file contains a list of various types of annotations that can be linked together with "Parent" and "ID" tags. py: use BCBio and BioPython to convert SAM file into GFF3 format. specify version=1 on a GTF or GFF3 file to interpret its 9-th column as the "group" column of a GFF1 file). It contains the basic gene annotation on the reference chromosomes, scaffolds, assembly patches and alternate loci (haplotypes) This is a subset of the corresponding comprehensive annotation, including only those transcripts tagged as 'basic' in every gene. Long non-coding RNA gene annotation. Sort GFF3 files, which can aid downstream processing and custom parsing (gff3_sort. NCBI’s GFF3 files differ from the official GFF3 specifications for certain attributes and formatting. You may grep LTR_retrotransposon *. to their respective locus, resulting in the desired number of isoforms for each locus. polycistronic) contained in a eukaryotic mRNA 5 Derive a GTF containing protein coding genes from a GTF file with Exons and CDS GFF2. gff3: As you can see, there is no gene, mRNA type info in the braker. To import a valid GFF3 file use the Import -> GFF3 file button to add annotation to the sequence. fasta is from NCBI as the gff3 file will use Chromosome IDs whereas the genome. I have the following GFF3 file which I would like to convert to ZFF file with the below script: $ head -n 20 traingenes. The GBFF format is based on the DDBJ/ENA/GenBank Feature Table Definition published by INSDC (International Nucleotide Sequence Database Collaboration). About file formats. Provide a list of splice sites (in the HISAT2's own format) as follows (four columns). Here is a brief description of the GFF fields: After this, you will get a new gff3 file: pyu_rnd3. Also, gff3_to_fasta can be used to generate six. Convert . It contains the basic gene annotation on the reference chromosomes, scaffolds, assembly patches and alternate loci (haplotypes) This is a subset of the corresponding comprehensive annotation, including only those transcripts tagged as 'basic' in every gene. Choosing which data files to include in the data package. 2. GRCh37. gff3. Comment. Abstract: The GFF3 format is a common, flexible tab-delimited format representing the structure and function of genes or other mapped features (this URL). mkdir 01_repeatModeler-denovo-repeat. gff > genes. As the title suggest, you will need your genome gff3 and fasta reference as inputs. For variants, rtracklayer has rudimentary support for. complement()[start:end] or should I use the reverse_complement()? Note that there is also a GFF3 specification that is not currently supported by the Browser. Effective as of human Updated Annotation Release 109. fa . funannotate util gff2tbl -g yourannot. This thread on biostars might help tho : Gff3 + Fasta To Genbank. GFF files. fa . makeTxDb is a low-level constructor for making a TxDb object from user supplied transcript annotations. gz input. 输入文件：只接受gene_predictions. If replace tags are present (see below), these tags must refer to transcript/mRNA. GRCh37 Genome Reference Consortium Human Build 37 (GRCh37) Organism: Homo sapiens (human) Submitter: Genome Reference Consortium Date: 2009/02/27 Assembly type: haploid-with-alt-loci Assembly level: Chromosome Genome representation: full Synonyms: hg19 GenBank assembly accession: GCA_000001405. 1. gtf同gff3很相似，也是9列内容，其内容如下： seqname: 序列的名字。通常格式染色体ID或是contig ID。 source：注释的来源。通常是预测软件名或是公共数据库。 feature：基因结构。CDS，start_codon，stop_codon是一定要含有的类型。 start：开始位点，从1开始计数。 end：结束. When the -e option is used (i. GFF2 has a number of shortcomings compared to GFF3. Note that GenBank prokaryotic or eukaryotic genomes can use GFF3 files in a GenBank-specific format as annotation input, as described at Annotating Genomes with GFF3 or GTF files. TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes - GitHub - zhangrengang/TEsorter: TEsorter: an accurate and fast method to classify LTR-retrotransposons in p. gt The GenomeTools genome analysis system. Rehydrate. Fasta files contain nucleotide or peptide sequences (nucleotides in the case of bacterial/archaeal genomes). gtf . We downloaded the GFF3 file and reformatted it for our. features # if an embedded ##FASTA directive is found, parse the sequences into gff. Saved searches Use saved searches to filter your results more quicklyALL. tappAS uses a gff3-like file with transcript structural and functional data. show program’s version number and exit. GFF2 (aka GTF) files can also be read: use GFF3 = FALSE to have the correct field names. TxDb objects have numerous accessors functions to allow such features to be. 3. Here, a stop_codon is only reported if the alignment reaches the C-terminus of the protein and the next codon is a stop codon. Unfortunately there have been many variations of the original GFF format and many have since become incompatible with each other. . GFF3 and GTF are the most widely used data formats for genomic annotations. py can be conceptually separated into 3 steps: Recognize or auto-assign Replace Tags to transcripts or mRNAs in the modified GFF3 file. For example $ h. The 9 columns are as follows. Jun2016. Note that GFF2 files and GFF3 files have the same structure, although some fields are slightly different (see reference). It is useful when genomic intervals around specific features and unique IDs are needed. Here is an example of what my gff file looks like: As you can see, my file clearly contains gff_type='CDS' entries. 3 is "Annotations in GFF format", which describes how to specify the proper tag indicating parent-child relationships. Based on the LD calculations previously computed and the r 2 threshold set by the user, annotations from a . Generate FASTA files from a GFF3 file for many use cases, e. Rgff also holds some other interesting utilities, like. How GFF3 attributes (9th column) varies from one gene prediction algorithm to another. eclipsed_orfs_removed. riparia grape de. Files in GFF3 format, on the other hand, contain annotations, a list of intervals corresponding to genes or other genomic features. GffRead and GffCompare. For GFF-Ex development, source code testing and analysis of package. htseq-count -f bam 31_36. Consequently, the output file will be a bed. Here, level 01 indicates that the element is manually annotated and experimentally verified. CottonFGD: an integrated functional genomics database for cotton. GFF has many versions, but the two most popular that are GTF2 (Gene Transfer Format, described. Replace the sequence IDs in a gff3 file with a set of provided sequence IDs from a genom. Featured on Meta We're rolling back the changes to the Acceptable Use Policy (AUP) Update: New Colors Launched. library (rtracklayer) ## import the bed file bed. ADD COMMENT • link updated 2. STAR uses the genome file (FASTA) and gene annotation file (GTF or GFF3) to create the genome indices. This is a superset of the main annotation file. ADD COMMENT • link 14 months ago Malcolm Cook ★ 1. seqid：参考序列的id。. This model can hold 40lbs of oil. gtf_to_gff3 Converts a GTF file into a GFF3 file Description This function converts a GTF file into a GFF3 file mantaining the feature hierarchy defined by the gene_id and transcript_id attributes. Ribosomal slippage. You can now retrieve genome data using the NCBI Datasets command-line tool and API by simply providing a BioProject accession. noseq. - GFF3-SOLiD calling format. Using pip. Are they supposed to be the same genome? Many of the entries in the GFF3 file, don't have the mandatory 'ID' attribute. JBrowse ia convenient way to view and distribute MAKER GFF3 output, and it comes with a simple script called maker2jbrowse that makes loading MAKER's output into JBrowse extremely easy. You can also choose to add additional data files or only include metadata in the data package using --include with one or more terms. The server has been upgraded with the lastest Python Packages2. Conclusions. If you have a troublesome file, the best thing to. The proposed GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats. 3,947 1 1 gold badge 6 6 silver badges 28 28 bronze badges $endgroup$ 1 $egingroup$ Thk for your awnser $endgroup$Genome annotation pipeline. Step 1: Configure a new genome in SnpEff's config file snpEff. $ python3 myscript. collapse_isoforms_by_sam. gff3. Use "gff3" or "gtf" only if auto-detection failed. life404 commented on Apr 12, 2022. Other GFF3 files of mixed data must be split by type and identified by the appropriate control file option (i. But when i try and convert this gff to a gtf using either genome tools (gt gff3_to_gtf my. . hg. 3 MB 12 FEB 2020 " 6 genomes 12 files, the first parameters are correct, but. LOCUS NW_023312688 196462 bp DNA linear CON 07-JUL-2020 DEFINITION Stegodyphus dumicola isolate AA2019 ecotype Namibia, Etosha unplaced genomic scaffold, ASM1061486v1 SEQ_00001, whole genome shotgun sequence. 1 gff3_QC readme 1 2 gff3_QC full documentation 5 3 gff3_fix readme 9 4 gff3_fix full documentation 11 5 gff3_merge readme 15 6 gff3_merge full documentation19 7 gff3_sort readme 27 8 gff3_to_fasta readme 33 9 FAQ 37 10 Indices and tables 41 i. $endgroup$ –GFF3格式文件为文本文件，分为9列，以TAB分开。. delim . We recommend using a GTF file instead of a GFF3 file, when possible. The X-axis label is "AED", and Y-axis label is "Cumulative Fraction of Annotations "Part 5. 1. In example 2 from above, the phase was 1, the corrected phase should be 2, but the phase remained 1 after running the script. e. I am using a self-made singularity container for this because I am running this on a large cluster. In the STAR manual, section 2. SOLiD BioScope generates genotype calls in GFF3 format, which we refer to as GFF3-SOLiD here. gtf ): the output just contains a header ( ##gff-version 2. JBrowse. 20200522 and mouse Updated Annotation Release 108. new addition – a model has. GFF has several versions, the most recent of which is GFF3. For species that have not been included in published database, annotation files could be prepared in a custom BED4/6 format. All the installed scripts have the agat_ prefix. Genome annotation files are provided in GFF3 format for all annotated assemblies included in NCBI’s Genomes FTP resource. 3. - GitHub - igvteam/igv-reports: Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files. gff3_parser. In the STAR manual, section 2. The tank on each model is embossed to reflect the correct oil level. In GenomicFeatures: Conveniently import and query gene models. py: Collapse HQ isoform results to unique isoforms (based. gff3sort. Unofficial attributes. The GFF3 specification can be found at the Sequence Ontology homepage, and there is a validator here. gz The output has 2 columns for genes near the SV start breakpoint and genes near the SV end breakpoint. The differences will be explained later in text. Incorporation of gff3. For each gene, the output lists the gene name and in paranthesis the distance (negative values: before SV breakpoint, 0: SV breakpoint within gene, positive values: after SV.