全基因组 - 生信小木屋

全基因组

Github开源生信云平台 DEMO

breseq: breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R. see
snippy: Rapid haploid variant calling and core genome alignment

学习资料

下载资源
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ref.fasta

GATK文献

2010年The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data是GATK的第一篇文章，它涵盖了GATK背后的计算哲学
2011年A framework for variation discovery and genotyping using next-generation DNA sequencing data最佳实践工作流程的首次体现，这是GATK的第二篇论文，更详细地描述了GATK中常用的一些关键工具，用于高通量测序数据处理和variant discovery。本文涵盖了碱基质量分数重新校准(base quality sore recalibration)、indel重新校准(realignment)、SNP calling with UnifiedGenotyper 、变异质量分数重新校正(variant quality score recalibration)及其在深层全基因组、全外显子组和低通多样本调用中的应用。如果您使用gatk进variant discovery，这是一个很好的引用
2013年From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline实践教程一步一步解释，这是GATK的第三篇论文，描述了Variant Discovery的最佳实践（version 2.x）。它主要是作为首次用户的学习资源和协议参考。最新的最贱时间是2020年的Genomics in the Cloud: Using Docker, GATK, and WDL in Terra。
2017年Scaling accurate genetic variant discovery to tens of thousands of samplesHaplotypeCaller的详细描述，germline joint calling的最佳参考，这是GATK的第四篇论文，如果在谈论联合调用过程（joint calling process），这是一个很好的引用。
2020年Genomics in the Cloud: Using Docker, GATK, and WDL in Terra这本书是使用GATK、Docker、WDL和Terra进行基因组学算法研究的权威参考。

Variant Analysis with GATK course (2019)

course materials

Introduction to GATK Workshop
Introduction to High-throughput Sequencing Data
Introduction to Data Preprocessing
Introduction to Variant Discovery
Introduction to Germline Variant Discovery
Introduction to Somatic Variant Discovery
Introduction to Pipelining Platforms
Introduction to a Case Study Analysis
Variant Calling with HaplotypeCaller
Joint Variant Calling
Variant Filtering by Variant Quality Score Recalibration
Genotype Refinement Workflow
Callset Evaluation
Introduction to Somatic Variant Discovery
Somatic SNVs and Indels Discovery
Pipelining with WDL and Cromwell
Hello World WDL Tutorial

BroadE: GATK (March 2019)

BroadE: GATK - Introduction to Training
BroadE: GATK - Introduction to High-Throughput Sequencing Data
BroadE: GATK - Introduction to Data Pre-processing
BroadE: GATK - Introduction to Variant Discovery
BroadE: GATK - Introduction to Pipeline Platforms
BroadE: GATK - Introduction to Germline Variant Discovery
BroadE: GATK - Haplotype Caller
BroadE: GATK - JointCalling
BroadE: GATK - Variant Filtering by Variant Quality Score Recalibration
BroadE: GATK - Genotype Refinement
BroadE: GATK - Callset Evaluation
BroadE: GATK - Intro to Somatic Variant Discovery
BroadE: GATK - Somatic SNVs and Indels
BroadE: GATK - Somatic Copy Number Alterations
BroadE: GATK - Pipelining with WDL and Cromwell