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README.md

高置信突变位点的整合

Author: Run Luyao

E-mail:18110700050@fudan.edu.cn

Git:http://choppy.3steps.cn/renluyao/high_confidence_calls_intergration.git

Last Updates: 12/6/2019

安装指南

# 激活choppy环境
source activate choppy
# 安装app
choppy install renluyao/high_confidence_calls_intergration

App概述

中华家系1号全基因组高置信small variants(SNVs和Indels)的整合流程。

Quartet家系的四个样本的DNA标准物质被送往多加测序公司,用PCRfree或者PCR的建库方法建立3个技术重复,用多个测序平台(Illumina XTen、Illumina Novaseq、BGISEQ-500、BGISEQ-2000和BGISEQ-T7)进行测序。获得的原始数据用多个分析流程进行分析(比对软件:BWA-mem、Novoalign、Bowtie2,突变检出软件:HaplotyperCaller、Strelka2、FreeBayes)。

经过以上各种因素的组合每个样本得到216个VCF文件,本APP的目的是整合这些VCF文件的结果得到一组可信度较高的突变。

流程与参数

App输入变量与输入文件

App输出文件

结果展示与解读

CHANGELOG

FAQ