生信喵 发表于 2023-6-16 20:18:10

GATK 简介

GATK 是 Genome Analysis ToolKit 的缩写,是一款从高通量测序数据中分析变异信息的软件,是目前最主流的 snp calling 软件之一。GATK 设计之初是用于分析人类的全外显子和全基因组数据,随着不断发展,现在也可以用于其他的物种,还支持 CNV 和 SV 变异信息的检测。在官网上,提供了完整的分析流程,叫做 GATK Best Practices。
      
      GATK 变异检测,从 fastq 到 vcf
      目前最新版本文为 4.0.4.0, 叫做 GATK4。和之前的版本相比,GATK4 在算法上进行了优化,运行速率有所提高,而且整合了 picard 软件的功能。GATK4 基于 java 语言开发的,需要 java1.8 版本。下载链接如下
https://github.com/broadinstitute/gatkGATK4 的最佳实践给出了 5 套 pipeline
      1、Germline SNPs + Indels
      2、Somatic SNVs + Indels
      3、RNAseq SNPs + Indels
      4、Germline CNVs
      5、Somatic CNVs

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