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肿瘤体细胞突变检测流程(组织、cfDNA均可,需要有对照)

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somatic_pipeline

肿瘤体细胞突变检测流程(组织、重复DNA均可,需要有对照)

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        {体细胞突变检测流程}
特点:
1)使用sentieon TNscope流程,准确、高效、快速
2)关联cosmic、www.cancergenomeinterpreter.org靶药数据库
3)分析SV,常见的融合基因一目了然
4)分析CNV,可检测拷贝数变异


输入:fastq

输出:somatic_mut.xlsx/tsv,SV,CNV,QC metrics...

使用方法:
        perl /gpfs/users/yanghao/project/somatic_pipeline/somatic.sentieon.fq.pipeline.pl -t  -t1  -t2  -n  -n1  -n2  -b 

默认提交到cn-medium分区,如果没有资源了,你可以指定作业提交到cn-fast,如下所示:
        perl /gpfs/users/yanghao/project/somatic_pipeline/somatic.sentieon.fq.pipeline.pl -t  -t1  -t2  -n  -n1  -n2  -b  -part cn-fast

如果你想在比对前,对fastq文件做一个trimming,可以这样:
        perl /gpfs/users/yanghao/project/somatic_pipeline/somatic.sentieon.fq.pipeline.pl -t  -t1  -t2  -n  -n1  -n2  -b  -trim 1

Last Updated:2017/12/29

Change Log
2017/12/29
支持trim(可选的,只要用了-trim 1,就会trim)
fix了一些perl环境变量、还有mosdepth的问题

如果使用过程中发生任何问题,请联系[email protected]

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肿瘤体细胞突变检测流程(组织、cfDNA均可,需要有对照)

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