======简介======
癌症的免疫基因组分析-新抗原预测分析
======功能======
对癌症样本进行新抗原预测
======脚本使用======
**1. 配置文件:**
config(需要带着表头,且不可写错):
SNV:
#SampleID Normal_Bam Maf_snv
LcaWzm_2 /TJPROJ11/GB_HUMAN/PJ_AI/cancer/WES/2002_new/X101SC2209/X101SC22093380-Z01/X101SC22093380-Z01-J001/Mapping/LcaWzm_1/LcaWzm_1.final.bam /TJPROJ11/GB_HUMAN/PJ_AI/cancer/WES/2002_new/X101SC2209/X101SC22093380-Z01/X101SC22093380-Z01-J001/Somatic/LcaWzm_2/muTect/LcaWzm_2.muTect.somatic.snv.maf
INDEL:
#SampleID Normal_Bam Maf_indel
LcaWzm_2 /TJPROJ11/GB_HUMAN/PJ_AI/cancer/WES/2002_new/X101SC2209/X101SC22093380-Z01/X101SC22093380-Z01-J001/Mapping/LcaWzm_1/LcaWzm_1.final.bam /TJPROJ11/GB_HUMAN/PJ_AI/cancer/WES/2002_new/X101SC2209/X101SC22093380-Z01/X101SC22093380-Z01-J001/Somatic/LcaWzm_2/Strelka/LcaWzm_2.Strelka.somatic.indel.maf
示例脚本:
SNV:
python /PUBLIC/software/Cancer/baiyingnan/01.Neoantigens/V2/HIM_v1.1.py \
--infile snv.config \
--analydir `pwd` \
--hlatype 1,2 \
--analy_array 1,2,4 \
--newjob snv_new.job \
INDEL:
python /PUBLIC/software/Cancer/baiyingnan/01.Neoantigens/V2/HIM_v1.1.py \
--infile indel.config \
--analydir `pwd` \
--hlatype 1,2 \
--analy_array 2,4 \
--newjob indel.job
运行脚本:
/TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/WES.X101SC22093380-Z01-J001.immune.20221102/HLA/snv.sh
/TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/WES.X101SC22093380-Z01-J001.immune.20221102/HLA/indel.sh
sh 刷脚本;
sjm先投递snv,再运行indel;
======交付结果======
HLA分型结果;
NEO新抗原检测结果;
示例路径:
/TJPROJ6/AFS_RESEQ/Proj/hanyue/06.gaoji/WES.X101SC22093380-Z01-J001.immune.20221102/HLA/Res-HLA