snpeff可以用于snp 和indel 文件的拆分，也可以用于注释这俩文件。
conda下载snpeff
conda activate python27
conda install -y snpeff #但其只下载到conda的pkgs文件夹，需要自己再软连接一下到conda的bin文件夹
Windows下下载jdk12，
conda下单独下载Java是困难的，那就换Windows，登录oracle下一个
https://link.zhihu.com/?target=https%3A//www.oracle.com/java/technologies/javase/jdk12-archive-downloads.html
ssh上传到服务器，Linux下解压“”
tar -zxvf jdk-12.0.2_linux-x64_bin.tar.gz
如果在没有jdk12的conda下唤醒snpeff，会报错
Error: A JNI error has occurred, please check your installation and try again
Exception in thread "main" java.lang.UnsupportedClassVersionError: org/snpeff/SnpEff has been compiled by a more recent version of the Java Runtime (class file version 55.0), this version of the Java Runtime only recognizes class file versions up to 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:756)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:468)
at java.net.URLClassLoader.access$100(URLClassLoader.java:74)
at java.net.URLClassLoader$1.run(URLClassLoader.java:369)
at java.net.URLClassLoader$1.run(URLClassLoader.java:363)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:362)
at java.lang.ClassLoader.loadClass(ClassLoader.java:418)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
at java.lang.ClassLoader.loadClass(ClassLoader.java:351)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:495)
解决方法
加入jdk12 和snpeff 到环境变量path
echo export PATH="/home/u20111230014/workspace/software/jdk-12.0.2:$PATH" >> ~/.bashrc
echo export PATH="/home/u20111230014/miniconda3/pkgs/snpeff-5.1-hdfd78af_0/share/snpeff-5.1-0:$PATH" >> ~/.bashrc
软连接到conda的bin 文件夹里面
ln -s /home/u20111230014/workspace/software/jdk-12.0.2/bin jdk12.02
ln -s /home/u20111230014/miniconda3/pkgs/snpeff-5.1-hdfd78af_0/share/snpeff-5.1-0/snpEff snpeff
jdk12应该写进哪里
root一般直接写进etc/profile, 非root用户不能修改etc/profile，只能将Jdk12写进 ~/.bashrc！！！
按顺序写进 ~/.bashrc
PS:一定要先写jdk, 再写snpeff, 因为snpeff需要jdk12来启动!!!
set java environment
JAVA_HOME=/home/u20111230014/workspace/software/jdk-12.0.2
CLASS_PATH=.:$JAVA_HOME/lib/dt.jar:$JAVA_HOME/lib/tools.jar
PATH=$PATH:$JAVA_HOME/bin
export JAVA_HOME CLASS_PATH PATH
export JAVA_HOME="/home/u20111230014/workspace/software/jdk-12.0.2"
export PATH=${JAVA_HOME}/bin:$PATH
export LD_LIBRARY_PATH=/home/u20111230014/workspace/software/jdk-12.0.2/lib/server:$LD_LIBRARY_PATH
export PATH=/home/u20111230014/workspace/software/jdk-12.0.2:/home/u20111230014/miniconda3/envs/python27/bin:/home/u20111230014/workspace/software/gatk-4.2.5.0:/home/u20111230014/miniconda3/conda/bin:/home/u20111230014/miniconda3/bin:/opt/app/r/4.1.1/bin:/usr/local/bin:/opt/app/r/4.1.1/bin:/home/public/software/miniconda2/bin:/opt/app/anaconda3/bin:/opt/app/conda/bin:/home/public/software/wfz_scripts:/opt/app/conda/bin:/opt/app/r/4.1.1/bin:/opt/app/spack/bin:/opt/app/spack/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/u20111230014/.local/bin:/home/u20111230014/bin
export PATH=/home/u20111230014/miniconda3/pkgs/snpeff-5.1-hdfd78af_0/share/snpeff-5.1-0:/home/u20111230014/miniconda3/envs/python27/bin:/home/u20111230014/miniconda3/pkgs
/snpeff-5.1-hdfd78af_0/share/snpeff-5.1-0:/home/u20111230014/miniconda3/envs/python27/bin:/home/u20111230014/workspace/software/gatk-4.2.5.0:/home/u20111230014/miniconda3
/condabin:/home/u20111230014/miniconda3/bin:/opt/app/r/4.1.1/bin:/usr/local/bin:/opt/app/r/4.1.1/bin:/home/public/software/miniconda2/bin:/opt/app/anaconda3/bin:/opt/app/
conda/bin:/home/public/software/wfz_scripts:/opt/app/conda/bin:/opt/app/r/4.1.1/bin:/opt/app/spack/bin:/opt/app/spack/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bi
n:/sbin:/bin:/home/u20111230014/.local/bin:/home/u20111230014/bin:/home/u20111230014/.local/bin:/home/u20111230014/bin
source ~/.bashrc 一下 搞定！
(python27) [u20111230014@cpu15 bin]$ snpeff
SnpEff version SnpEff 5.1 (build 2022-01-21 06:23), by Pablo Cingolani
Usage: snpEff [command] [options] [files]
Run 'java -jar snpEff.jar command' for help on each specific command
Available commands:
[eff|ann] : Annotate variants / calculate effects (you can use either 'ann' or 'eff', they mean the same). Default: ann (no command or 'ann').
build : Build a SnpEff database.
buildNextProt : Build a SnpEff for NextProt (using NextProt's XML files).
cds : Compare CDS sequences calculated form a SnpEff database to the one in a FASTA file. Used for checking databases correctness.
closest : Annotate the closest genomic region.
count : Count how many intervals (from a BAM, BED or VCF file) overlap with each genomic interval.
databases : Show currently available databases (from local config file).
download : Download a SnpEff database.
dump : Dump to STDOUT a SnpEff database (mostly used for debugging).
genes2bed : Create a bed file from a genes list.
len : Calculate total genomic length for each marker type.
pdb : Build interaction database (based on PDB data).
protein : Compare protein sequences calculated form a SnpEff database to the one in a FASTA file. Used for checking databases correctness.
seq : Show sequence (from command line) translation.
show : Show a text representation of genes or transcripts coordiantes, DNA sequence and protein sequence.
translocReport : Create a translocations report (from VCF file).
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)
后记：
可能不是root，不能写进profile的原因，想在conda特定环境下唤醒snpEff，最好在conda下开一个环境给最高版本的Java
conda create -n java12
conda activate java12
conda install openjdk=12.0.2 # 直接在conda下安装openjdk=12.0.2，总下载不了
##换一种方式，这个rjava下载完是版本11.0.9.1
conda install -c r r-rjava
(java12) [u20111230014@cpu15 snpeff-5.1-1]$ java -version
openjdk version "11.0.9.1-internal" 2020-11-04
OpenJDK Runtime Environment (build 11.0.9.1-internal+0-adhoc..src)
OpenJDK 64-Bit Server VM (build 11.0.9.1-internal+0-adhoc..src, mixed mode)
##足够能带动snpEff就行
conda install -y snpeff ##下载后启动snpEff
(java12) [u20111230014@cpu15 snpeff-5.1-1]$ whereis snpEff
snpEff: /home/u20111230014/miniconda3/envs/java12/bin/snpEff /home/u20111230014/miniconda3/pkgs/snpeff-5.1-hdfd78af_0/share/snpeff-5.1-0/snpEff /home/u20111230014/miniconda3/pkgs/snpeff-5.1-hdfd78af_0/share/snpeff-5.1-0/snpEff.config /home/u20111230014/miniconda3/pkgs/snpeff-5.1-hdfd78af_0/share/snpeff-5.1-0/snpEff.jar /home/u20111230014/miniconda3/envs/python27/bin/snpEff
