<![CDATA[突变分析]]>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
92f831ae-da24-4f83-9b1e-31eee32849f0-image.png

2.分析流程
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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

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