pre-processing reads and non-model BQSR
Hi! I’m trying to plan my GATK pipeline and have a few questions. We currently have an assembled genome for a non-model avian species and would like to align the reads from the single individual to the...
View Articledisable strand bias and clustered position filters, mutect
Hi, I would like to analyze a dataset consisting of RADseq (Restriction-site Associated DNA) tags from tumor and normal samples. With Radseq, the reads start at restriction enzyme cut sites in the...
View ArticleProblem in calculating Depth of Coverage using GenomeAnalysisTK.jar
I am using this command to calculate the depth of coverage with three different formats for the EXOME_interval.list : java -Xmx2048m -jar GenomeAnalysisTK.jar -T DepthOfCoverage -I...
View ArticleClik here to view.
Best Practice Variant Detection with the GATK v4, for release 2.0
Introduction 1. The basic workflow Our current best practice for making SNP and indel calls is divided into four sequential steps: initial mapping, refinement of the initial reads, multi-sample indel...
View ArticleHow should I interpret VCF files produced by the GATK?
1. What is VCF? VCF stands for Variant Call Format. It is a standardized text file format for representing SNP, indel, and structural variation calls. See this page for detailed specifications. VCF is...
View ArticleWhat's in the resource bundle and how can I get it?
1. Obtaining the bundle Inside of the Broad, the latest bundle will always be available in: /humgen/gsa-hpprojects/GATK/bundle/current with a subdirectory containing for each reference sequence and...
View ArticleHow can I access the GSA public FTP server?
We make various files available for public download from the GSA FTP server, such as the GATK resource bundle and presentation slides. We also maintain a public upload feature for processing bug...
View ArticleWhat VQSR training sets / arguments should I use for my specific project?
VariantRecalibrator For use with calls generated by the UnifiedGenotyper The variant quality score recalibrator builds an adaptive error model using known variant sites and then applies this model to...
View ArticleWhat input files does the GATK accept?
1. Reference Sequence The GATK requires the reference sequence in a single reference sequence in FASTA format, with all contigs in the same file. The GATK requires strict adherence to the FASTA...
View ArticleHow to run Queue for the first time
Objective Run a basic analysis command on example data, parallelized with Queue. Prerequisites Successfully completed "How to test your Queue installation" and "How to run GATK for the first time" GATK...
View ArticleOverview of Queue
1. Introduction GATK-Queue is command-line scripting framework for defining multi-stage genomic analysis pipelines combined with an execution manager that runs those pipelines from end-to-end. Often...
View ArticleHow can I prepare a FASTA file to use as reference?
The GATK uses two files to access and safety check access to the reference files: a .dict dictionary of the contig names and sizes and a .fai fasta index file to allow efficient random access to the...
View ArticlePipelining the GATK with Queue
1. Introduction As mentioned in the introductory materials, the core concept behind the GATK tools is the walker. The Queue scripting framework contains several mechanisms which make it easy to chain...
View ArticleClik here to view.
What is GATK-Lite and how does it relate to "full" GATK 2.x?
You probably know by now that GATK-Lite is a free-for-everyone and completely open-source version of the GATK (licensed under the original MIT license). But what's in the box? What can GATK-Lite do --...
View ArticleParallelism with the GATK - RETIRED
This article is out of date and has been replaced by updated documents: - Primer on parallelism - Specific usage recommendations The old document, for archival purposes: 1. Overview The MapReduce...
View ArticleWhat is Map/Reduce and why are GATK tools called "walkers"?
Overview One of the key challenges of working with next-gen sequence data is that input files are usually very large. We can’t just make the program open the files, load all the data into memory and...
View ArticleFrequently asked questions about Scala
1. What is Scala? Scala is a combination of an object oriented framework and a functional programming language. For a good introduction see the free online book Programming Scala. The following are...
View ArticleWriting walkers
1. Introduction The core concept behind GATK tools is the walker, a class that implements the three core operations: filtering, mapping, and reducing. filter Reduces the size of the dataset by applying...
View ArticleCollected FAQs about BAM files
1. What file formats do you support for sequencer output? The GATK supports the BAM format for reads, quality scores, alignments, and metadata (e.g. the lane of sequencing, center of origin, sample...
View ArticleQueue pipeline scripts (QScripts)
1. Introduction Queue pipelines are Scala 2.8 files with a bit of syntactic sugar, called QScripts. Check out the following as references. http://programming-scala.labs.oreilly.com...
View Article
![[-100%] Commodity Intelligence – (Android Apps)](http://play-lh.googleusercontent.com/j67-qJvmnn4xnVlYVZ9ZhtZUJIgwjKekJGoKQT6D1KHcWGZxtQaFroummEvwV17na7tyh1pGbbeWCRdWtTKqeg=w950-h950)
