gatk4的安装与下载

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已于 2024-05-16 17:51:44 修改

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于 2023-06-26 17:19:42 首次发布

本文链接：https://blog.csdn.net/hgz2020/article/details/131398873

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GATK4 的最新版本4.4.0.0引入了重大更新，包括迁移至Java 17作为构建和运行的最新长期支持版本，新增工具，如GenotypeConcordance，并在SelectVariants中支持GVCF过滤。此外，还修复了多个错误并提升了对流式变异呼叫和结构变异调用的支持。

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1. 下载安装包

点击下载 gatk4下载网址，其对应的版本是gatk4-4.4.0.0.zip

wget https://github.com/broadinstitute/gatk/releases/download/4.2.1.0/gatk-4.4.0.0.zip #下载安装包
unzip gatk-4.2.1.0 #解压缩安装包
cd gatk-4.2.1.0/
ls -hlt #查看安装包内容
echo "PATH=$PATH:/gatk-4.2.1.0/path" >>~/.bashrc
source ~/.bashrc
gatk -h  #检查是否可正常运行

2. 功能更新说明

4.4.0.0

Download release: gatk-4.4.0.0.zip
Docker image: https://hub.docker.com/r/broadinstitute/gatk/

Highlights of the 4.4.0.0 release:

We've moved to Java 17, the latest long-term support (LTS) Java release, for building and running GATK! Previously we required Java 8, which is now end-of-life.
- Newer non-LTS Java releases such as Java 18 or Java 19 may work as well, but since they are untested by us we only officially support running with Java 17.
Significant enhancements to SelectVariants, including arguments to enable GVCF filtering support and to work with genotype fields more easily.
A new tool SVConcordance, that calculates SV genotype concordance between an "evaluation" VCF and a "truth" VCF
Bug fixes and enhancements to the support for the Ultima Genomics flow-based sequencing platform introduced in GATK 4.3.0.0

Full list of changes:

Flow-based Variant Calling
- FlowFeatureMapper: added surrounding-median-quality-size feature (#8222)
- Removed hardcoded limit on max homopolymer call (#8088)
- Fixed bug in dynamic read disqualification (#8171)
- Fixed a bug in the parsing of the T0 tag (#8185)
- Updated flow-based calling Mutect2 parameters to make them consistent with the HaplotypeCaller parameters (#8186)
SelectVariants
- Enabled GVCF type filtering support in SelectVariants (#7193)
  - Added an optional argument --ignore-non-ref-in-types to support correct handling of VariantContexts that contain a NON_REF allele. This is necessary because every variant in a GVCF file would otherwise be assigned the type MIXED, which ma