snpeff注释

cd /public/jychu/zhengxt/ovis_aries_genome/VCF/cjy_result
mkdir soft
cd soft
wget http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip
unzip snpEff_latest_core.zip
修改 snpEff 目录下的注释文件 snpEff.config，在“Third party databases”行下加入如下内容：
#  sheep genome, version Oar_rambouillet_v1.0
Oar_rambouillet_v1.0.genome : sheep
在 snpEff 目录下，创建目录 data, data/Oar_rambouillet_v1.0, data/genomes
mkdir -p data data/Oar_rambouillet_v1.0 data/genomes
将 gtf 文件放入Oar_rambouillet_v1.0目录下，并改名为 genes.gtf；将基因组序列文件放入 genomes 目录下，并改名为 Oar_rambouillet_v1.0.fa
cp /public/jychu/zhengxt/refs/Ovis_aries_rambouillet.Oar_rambouillet_v1.0.101.gtf /public/jychu/zhengxt/ovis_aries_genome/VCF/cjy_result/soft/snpEff/data/Oar_rambouillet_v1.0
mv Ovis_aries_rambouillet.Oar_rambouillet_v1.0.101.gtf genes.gtf
cp /public/jychu/zhengxt/refs/Ovis_aries_rambouillet.Oar_rambouillet_v1.0.dna.toplevel.fa /public/jychu/zhengxt/ovis_aries_genome/VCF/cjy_result/soft/snpEff/data/genomes
mv Ovis_aries_rambouillet.Oar_rambouillet_v1.0.dna.toplevel.fa Oar_rambouillet_v1.0.fa
数据库建立:在 snpEff 目录下，执行命令：
java -jar snpEff.jar build -gtf22 -v Oar_rambouillet_v1.0   #如果成功那么在Oar_rambouillet_v1.0目录下会有一个".bin"文件产生
对vcf格式文件进行注释：
cd /public/jychu/zhengxt/ovis_aries_genome/VCF/cjy_result/soft/snpEff/data
java -Xmx16g -jar /public/jychu/zhengxt/ovis_aries_genome/VCF/cjy_result/soft/snpEff/snpEff.jar eff -v Oar_rambouillet_v1.0  -c /public/jychu/zhengxt/ovis_aries_genome/VCF/cjy_result/soft/snpEff/snpEff.config -i vcf /public/jychu/zxt_sheep/SNP_analysis/sheep.analysis_zk_tc.dbsnp1.vcf  >/public/jychu/zxt_sheep/SNP_analysis/sheep.analysis_zk_tc.dbsnp1_zs.vcf
bgzip sheep.analysis_zk_tc.dbsnp1_zs.vcf