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README.md

Extract BAM for IGV

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

samtools view -b ${bam} "${region}" > ${region}.${sample}.bam
samtools index ${region}.${sample}.bam

samples文件中的region格式如下:

#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