目录

1.帮助文档

1.1 常用参数

2. 命令的用法：

3. 结果文件解读

4. SNP下游的分析

---

利用snpEff软件对 snp.vcf （利用gatk软件calling-snp）进行注释，运行下述命令：

## 构建好物种的数据库
java -jar /opt/snpEff/snpEff.jar build -c ./snpEff.config  -gtf22 -v Ath10M
## 进行注释
java -jar /opt/snpEff/snpEff.jar -c  ./snpEff.config -ud 5000 -csvStats test.csv -htmlStats test.html -o vcf  Ath10M  ../data/all.filtered.snp.vcf > all.filtered.snp.ann.vcf

1.帮助文档

java -jar /data/home/hgzhong/home/software_set/snpeff/snpEff/snpEff.jar --help

##参数
Options:
	-chr <string>                   : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
	-classic                        : Use old style annotations instead of Sequence Ontology and Hgvs.
	-csvStats <file>                : Create CSV summary file.
	-download                       : Download reference genome if not available. Default: true
	-i <format>                     : Input format [ vcf, bed ]. Default: VCF.
	-fileList                       : Input actually contains a list of files to process.
	-o <format>                     : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
	-s , -stats, -htmlStats         : Create HTML summary file.  Default is 'snpEff_summary.html'
	-noStats                        : Do not create stats (summary) file

Results filter options:
	-fi , -filterInterval  <file>   : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
	-no-downstream                  : Do not show DOWNSTREAM changes
	-no-intergenic                  : Do not show INTERGENIC changes
	-no-intron                      : Do not show INTRON changes
	-no-upstream                    : Do not show UPSTREAM changes
	-no-utr                         : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
	-no <effectType>                : Do not show 'EffectType'. This option can be used several times.

Annotations options:
	-cancer                         : Perform 'cancer' comparisons (Somatic vs Germline). Default: false
	-cancerSamples <file>           : Two column TXT file defining 'oringinal \t derived' samples.
	-fastaProt <file>               : Create an output file containing the resulting protein sequences.
	-formatEff                      : Use 'EFF' field compatible with older versions (instead of 'ANN').
	-geneId                         : Use gene ID instead of gene name (VCF output). Default: false
	-hgvs                           : Use HGVS annotations for amino acid sub-field. Default: true
	-hgvsOld                        : Use old HGVS notation. Default: false
	-hgvs1LetterAa                  : Use one letter Amino acid codes in HGVS notation. Default: false
	-hgvsTrId                       : Use transcript ID in HGVS notation. Default: false
	-lof                            : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
	-noHgvs                         : Do not add HGVS annotations.
	-noLof                          : Do not add LOF and NMD annotations.
	-noShiftHgvs                    : Do not shift variants according to HGVS notation (most 3prime end).
	-oicr                           : Add OICR tag in VCF file. Default: false
	-sequenceOntology               : Use Sequence Ontology terms. Default: true

Generic options:
	-c , -config                 : Specify config file
	-configOption name=value     : Override a config file option
	-d , -debug                  : Debug mode (very verbose).
	-dataDir <path>              : Override data_dir parameter from config file.
	-download                    : Download a SnpEff database, if not available locally. Default: true
	-nodownload                  : Do not download a SnpEff database, if not available locally.
	-h , -help                   : Show this help and exit
	-noLog                       : Do not report usage statistics to server
	-q , -quiet                  : Quiet mode (do not show any messages or errors)
	-v , -verbose                : Verbose mode
	-version                     : Show version number and exit

Database options:
	-canon                       : Only use canonical transcripts.
	-canonList <file>            : Only use canonical transcripts, replace some transcripts using the 'gene_id 	 transcript_id' entries in <file>.
	-interaction                 : Annotate using inteactions (requires interaciton database). Default: true
	-interval <file>             : Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times)
	-maxTSL <TSL_number>         : Only use transcripts having Transcript Support Level lower than <TSL_number>.
	-motif                       : Annotate using motifs (requires Motif database). Default: true
	-nextProt                    : Annotate using NextProt (requires NextProt database).
	-noGenome                    : Do not load any genomic database (e.g. annotate using custom files).
	-noExpandIUB                 : Disable IUB code expansion in input variants
	-noInteraction               : Disable inteaction annotations
	-noMotif                     : Disable motif annotations.
	-noNextProt                  : Disable NextProt annotations.
	-onlyReg                     : Only use regulation tracks.
	-onlyProtein                 : Only use protein coding transcripts. Default: false
	-onlyTr <file.txt>           : Only use the transcripts in this file. Format: One transcript ID per line.
	-reg <name>                  : Regulation track to use (this option can be used add several times).
	-ss , -spliceSiteSize <int>  : Set size for splice sites (donor and acceptor) in bases. Default: 2
	-spliceRegionExonSize <int>  : Set size for splice site region within exons. Default: 3 bases
	-spliceRegionIntronMin <int> : Set minimum number of bases for splice site region within intron. Default: 3 bases
	-spliceRegionIntronMax <int> : Set maximum number of bases for splice site region within intron. Default: 8 bases
	-strict                      : Only use 'validated' transcripts (i.e. sequence has been checked). Default: false
	-ud , -upDownStreamLen <int> : Set upstream downstream interval length (in bases)

1.1 常用参数

-ud, updownStreamLen ：距离SNP位点上下游的长度

java -jar： Java环境下运行程序

-c，-config： snpEff.config配置文件路径（此处的是将其复制至当前目录）

-gff3 ：设置输入基因组注释信息是gff3格式，如果是gtf文件请改为-gtf22

-v ,-verbose：设置在程序运行过程中输出的日志信息，设置输入的基因组版本信息，和snpEff.config配置文件中添加的信息一致

-o :输出文件格式

2. 命令的用法：

Usage: snpEff [eff] [options] genome_version [input_file]

##例子
java -jar /opt/snpEff/snpEff.jar -c  ./snpEff.config -ud 5000 -csvStats test.csv -htmlStats test.html -o vcf  Ath10M  ../data/all.filtered.snp.vcf > all.filtered.snp.ann.vcf

3. 结果文件解读

获得的结果文件：

test.csv
test.html
test.genes.txt
all.filtered.snp.ann.vcf

*.ann.vcf 是一个注释结果文件，其就在vcf的info信息新添加了anno一列信息，其具体每个值含义如下：
Allele
　　突变之后的碱基，第一个突变位点由T碱基突变成了C碱基，对应Allel的值为C
Annotation
　　由sequence ontology定义的突变类型
Annotation_Impact
　　对变异位点有害程度的简单评估，取值有HIGH, MODERATE, LOW, MODIFIER 4种，含义如下

 

查看 test.genes.txt 文件：

 

1 染色体
2 突变位置
3 突变周边，“.”的右边时突变位置
4 参考碱基
5 突变碱基
6 是否通过过滤
7 突变类型，氨基酸变化，上下游、基因间、内含子的突变情况
8 参考时0
9/10 不突变0，突变1

第七列详情，任取三个突变

 

结果 test.html 文件：

 

 

 注释结果的HTML文件的详情解读请参照 snpeff结果解读

 

4. SNP下游的分析

可以使用snpEff注释的vcf进行4DTv位点分析，然后用其构建进化树。
或者是直接使用vcf构建进化树。
两种方法构建进化树均已经实现流程自动化。Vcf2Tree github