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mtDNA_Pipeline 说明文档

Author: MatthewP

服务器： 深圳服务器

脚本地址： /ifs1/Reotech/user/pengguoyu/mtDNA

项目执行地址： /ifs1/Reotech/project/mtDNA/

操作步骤

  1. 进入项目地址：/ifs1/Reotech/project/mtDNA/
  2. 按照当天日期建立文件夹，比如：mkdir 20180613
  3. 编辑shell脚本，比如vim mtDNA.sh
  4. shell脚本内容示范如下：

python /ifs1/Reotech/user/pengguoyu/mtDNA/mtDNA_Pipeline.py -s "20180613/RunByWDL/BB5118402-18524A-A019V1-PM4-XX-18R07049,20180613/RunByWDL/BB5118402-18524A-A019V1-PM4-XX-18R07050,20180613/RunByWDL/BB5118402-18 524A-A019V1-PM4-XX-18R07051,20180613/RunByWDL/BB5118402-18524A-A019V1-PM4-XX-18R07052,20180613/RunByWDL/BB5118402-18524A-A019V1-PM4-XX-18R07053,20180613/RunByWDL/BB5118402-18524A-A019V1-PM4-XX-18R07054,20180613/RunByWDL/BB5118402-18524A-A019V1-PM4-XX-18R07055,20180613/RunByWDL/BB5118402-18524A-A019V1-PM4-XX-18R07056,20180613/RunByWDL/BB5118402-18524A-A019V1-PM4-XX-18R07057,20180613/RunByWDL/BB5118402-18524A-A019V1-PM4-XX-18R07058" -l "18R07049,18R07050,18R07051,18R07052,18R07053,18R07054,18R07055,18R07056,18R07057,18R07058" -n /ifs1/Reotech/project/mtDNA/20180613/RunByWDL/18R070 -o /ifs1/Reotech/project/mtDNA/20180613/RunByWDL/inputs.json

  1. 保存并运行shell脚本：sh mtDNA.sh
  2. 最终结果文件为-n参数加上_result.vcf文件。如-n参数为/ifs1/Reotech/project/mtDNA/20180613/RunByWDL/18R070 那么最终结果文件为/ifs1/Reotech/project/mtDNA/20180613/RunByWDL/18R070_result.vcf

脚本说明

shell脚本调用了 /ifs1/Reotech/user/pengguoyu/mtDNA/mtDNA_Pipeline.py mtDNA_Pipeline.py 建议使用python3.6+运行，需要4个参数:

  • -s Rawdata的部分路径，比如：/ifs1/Reotech/project/mtDNA/ 20180613/RunByWDL/BB5118402-18524A-A019V1-PM4-XX-18R07058 _R1.fastq.gz 取加粗部分即可，前面的项目路径 /ifs1/Reotech/project/mtDNA/和后面的\_R1.fastq.gz

或者\_R2.fastq.gz部分不需要,脚本会将那些部分补齐。一次运行多个样品的时候，将多个样品放在同一个字符串下，样品间用","分隔。

  • -l 样品ID，由于 Varscan2 进行virant call的时候，无法正确获取样品名，需要将样品ID用列表形式写在文件里，传给 Varscan2 同-s一样，按照顺序将样品ID放在同一个字符串，用","进行分割。~~ 注意 ~~：这里样品ID顺序需要和-s的Rawdata顺序一致！

  • -n 在 samtools mpileup 后，所有的样品被合并为一个样品，直至整个流程结束。往后样品， 需要一个样品路径与基础名字。比如 /ifs1/Reotech/project/mtDNA/20180613/RunByWDL/ 18R070其中加粗部分为路径，18R070为文件基础名字，后续步骤将按此产生各步文件，比如：/ifs1/Reotech/project/mtDNA/20180613/RunByWDL/18R070_snpEff.vcf 或者: /ifs1/Reotech/project/mtDNA/20180613/RunByWDL/18R070_result.vcf

-o mtDNA_Pipeline.py 会调用 mtDNA_Pipeline.wdl，而mtDNA_Pipeline.wdl 需要一个json文件作为inputs配置，这里需要指定该文件地址(python)脚本会生成该json，仅仅指定地址即可。比如： /ifs1/Reotech/project/mtDNA/20180613/RunByWDL/inputs.json