readme

README.md

+# DELLY Somatic Mutation Calling
+
+> Author： Ren Luyao
+>
+> E-mail：18110700050@fudan.edu.cn
+>
+> Git: http://choppy.3steps.cn/renluyao/IGV_get_bam.git
+>
+> Last Updates: 2020/0705
+
+## 安装指南
+
+```
+# 激活choppy环境
+source activate choppy
+# 安装app
+choppy install renluyao/IGV_get_bam
+```
+
+## App概述
+
+为了IGV验证突变，截取其中一段bam文件
+
+## 流程与参数
+
+```bash
+samtools view -b ${bam} "${region}" > ${region}.${sample}.bam
+samtools index ${region}.${sample}.bam
+```
+
+samples文件中的region格式如下：
+
+```bash
+#chromo:start-end
+chr6:73900000-73920000
+```
+
+## App输出文件
+
+输出结果为截取的bam文件和相应的bam索引文件

inputs

   "{{project_name }}.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc",
   "{{project_name }}.bam": "{{ bam }}",
   "{{project_name }}.sample": "{{ sample }}"
-}
+}
+