=====rnaindel=====

网址https://github.com/stjude/RNAIndel，已经安装/TJPROJ6/RNA_SH/personal_dir/zhangxin/miniconda/envs/py36/bin/rnaindel.下载数据路径/TJPROJ6/RNA_SH/script_dir/RNAIndel_database/data_dir_grch38

RNAIndel calls coding indels from tumor RNA-Seq data and classifies them as somatic, germline, and artifactual. RNAIndel supports GRCh38 and 37.

先是用star比对，如下：
  export PYTHONPATH=""
  
  unset PERL5LIB
  
  export PATH=/TJPROJ2/GB/PUBLIC/software/GB_TR/mRNA/miniconda3/envs/QC/bin:$PATH
  
  export LD_LIBRARY_PATH=/TJPROJ2/GB/PUBLIC/software/GB_TR/mRNA/miniconda3/envs/QC/bin/../lib:$LD_LIBRARY_PATH
  
  export JAVA_HOME=/TJPROJ2/GB/PUBLIC/software/GB_TR/mRNA/miniconda3/envs/QC/bin/..
  
  STAR --runThreadN 4 --genomeDir /TJPROJ6/RNA_SH/script_dir/RNAIndel_database --readFilesIn /TJPROJ6/RNA_SH/shouhou/202205/MuTect2-test/QC/Treatment_1/Treatment_1_1.clean.fq.gz /TJPROJ6/RNA_SH/shouhou/202205/MuTect2-test/QC/Treatment_1/Treatment_1_2.clean.fq.gz --readFilesCommand zcat --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMismatchNmax 2 --outReadsUnmapped Fastx --twopassMode Basic --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --alignSJstitchMismatchNmax 5 -1 5 5 --chimOutJunctionFormat 1 --outFileNamePrefix /TJPROJ6/RNA_SH/shouhou/202205/MuTect2-test/RNAIndel/Treatment_1 --outTmpDir /TJPROJ6/RNA_SH/shouhou/202205/MuTect2-test/RNAIndel/tmp
  
  STAR --runThreadN 4 --genomeDir /TJPROJ6/RNA_SH/script_dir/RNAIndel_database --readFilesIn /TJPROJ6/RNA_SH/shouhou/202205/MuTect2-test/QC/Control_1/Control_1_1.clean.fq.gz /TJPROJ6/RNA_SH/shouhou/202205/MuTect2-test/QC/Control_1/Control_1_2.clean.fq.gz --readFilesCommand zcat --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMismatchNmax 2 --outReadsUnmapped Fastx --twopassMode Basic --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --alignSJstitchMismatchNmax 5 -1 5 5 --chimOutJunctionFormat 1 --outFileNamePrefix /TJPROJ6/RNA_SH/shouhou/202205/MuTect2-test/RNAIndel/Control_1 --outTmpDir /TJPROJ6/RNA_SH/shouhou/202205/MuTect2-test/RNAIndel/tmp1

测试如下：
  source activate /TJPROJ6/RNA_SH/personal_dir/zhangxin/miniconda/envs/py36
  
  rnaindel PredictIndels -i /TJPROJ6/RNA_SH/shouhou/202205/MuTect2-test/RNAIndel/Treatment_1Aligned.sortedByCoord.out.bam -o test.vcf -r /TJPROJ6/RNA_SH/script_dir/RNAIndel_database/chr_Homo_sapiens_Ensemble_94.fa -d /TJPROJ6/RNA_SH/script_dir/RNAIndel_database/data_dir_grch38  -p 8
  
  rnaindel PredictIndels -i /TJPROJ6/RNA_SH/shouhou/202205/MuTect2-test/RNAIndel/Control_1Aligned.sortedByCoord.out.bam -o test1.vcf -r /TJPROJ6/RNA_SH/script_dir/RNAIndel_database/chr_Homo_sapiens_Ensemble_94.fa -d /TJPROJ6/RNA_SH/script_dir/RNAIndel_database/data_dir_grch38  -p 8
  
最终，本次测试结果vcf中没有结果，oe文件中不存在报错，后续可以再进行测试。
github中的测试数据下载需要登入账号，无法下载。