突变分析

[anneng]

突变分析涉及众多软件　以GATK　best pratices　流程来进行说明：
对相同物种、近似物种的不同个体进行测序叫重测序。这些物种都需要有参考基因组，因此不需要组装步骤。应用场景包括：肿瘤组织和正常组织，父代和子代。
涉及的软件主要有：bwa picard bamtools gatk samtools bcftools vcftools

1.序列的类型

2.分析流程

2.1　比对

bwa bowtie
输出的格式为SAM　转化为二进制的话为BAM
BAM文件可以通过很多文件进行处理
SAMtools -- provides various utilities for manipulating alignments in the SAM and
BAM format, including sorting, merging, indexing and generating
alignments in a per-position format.
Picard -- – comprises Java-based command-line utilities that manipulate SAM and
BAM files
GATK -- GATK offers a wide variety of tools, with a primary focus on variant
discovery and genotyping as well as strong emphasis on data quality
assurance.
IGV -- is very useful for visualizing mapped reads