sh /TJPROJ6/RNA_SH/personal_dir/liuyan/2022_03/run.sh

需要在run.sh内修改部分读入文件

第一步：/PUBLIC/software/public/System/jre1.8.0_25/bin/java -jar -Xmx12G -XX:ParallelGCThreads=6 /TJPROJ6/RNA_T/software/snpeff/snpeff-4.3q/snpEff/snpEff.jar -v Mus_musculus_Ensemble_94 -c /TJPROJ6/RNA_SH/personal_dir/liuyan/2022_03/snpEff.config -stats WT_12m_1_stat.html -csvStats WT_12m_1_stat.csv WT_12m_1.vcf > WT_12m_1_snpeff.vcf
-v 物种参考基因组
-stats 样品.html
-csvStats 样品.csv
样品.vcf >样品.snpeff.vcf 

第二步：perl /TJPROJ6/RNA_SH/personal_dir/liuyan/2022_03/change_snpeffToMaf.pl 样品.snpeff.vcf > 样品.maf