The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. Its scope is now expanding to include somatic short variant calling, and to tackle copy number (CNV) and structural variation (SV).

GATK4 aims to bring together well-established tools from the GATK and Picard codebases under a streamlined framework, and to enable selected tools to be run in a massively parallel way on local clusters or in the cloud using Apache Spark. It also contains many newly developed tools not present in earlier releases of the toolkit.

2024年7月20日 · We provide end-to-end workflows, called GATK Best Practices, tailored for specific use cases. Starting with version 4.0, GATK contains a copy of the Picard toolkit, so all Picard tools are available from within GATK itself. Their documentation is available in the Tool Index section of this website. 1. Preview the pipelines.

The Genome Analysis Toolkit (GATK) is a structured programming framework designed to enable the rapid development of efficient and robust analysis tools for next-generation DNA sequencers.

What is physical phasing? Where can I get the GATK source code? Is it open-source? Are there Best Practices for calling variants in RNAseq data? Does GATK work on non-diploid organisms?

在GATK HaplotypeCaller之后，首选的质控方案是GATK VQSR， 原理是利用自身数据和已知变异位点集的overlap，通过GMM模型构建一个分类器来对变异数据进行打分，从而评估每个位点的可行度。

2018年1月9日 · Today the Broad Institute of MIT and Harvard is releasing version 4.0 of the Genome Analysis Toolkit (GATK), the institute's flagship genome variant discovery package for analysis of high-throughput sequencing data.

Updated the GATK base docker image to Ubuntu 22.04 for security fixes and newer versions of genomics packages like samtools and bcftools ; Updated GATK dependencies to address known security vulnerabilities, and added a vulnerability scanner …

2024年2月15日 · The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. Its scope is now expanding to include somatic short variant calling, and to tackle copy number (CNV) and structural variation (SV).

2023年11月20日 · Overview: Understand GATK as a versatile toolkit for variant discovery and genotyping from high-throughput sequencing data, developed by the Broad Institute. Workflow Overview: Explore the typical GATK workflow involving read mapping, duplicate marking, base quality recalibration, variant calling, and variant filtering.