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This commit was created on GitHub. We now report the same value as ExcHet in bcftools. Note that previous values of 3.

Updated ExcessHet documentation. Miscellaneous Changes Delete an unused. Assets 3 gatk This resulted in variants that were called and not filtered, but they should have been filtered by "germline". The fix avoids the crash by adding additional bounds checking. Logic for producing representative records from a collection of clustered SVs has been separated into an SVCollapser class, which provides enhanced functionality for handling genotypes for SVs more generally.

These fields are now each stored as a String. This allows for arbitrary values in these fields and will help to future-proof and species-proof the GTF parser. In this case, the code will no longer throw a user exception, but will log a warning and will produce? Added AminoAcid. Funcotator now checks whether the input has already been annotated, and by default throws an error in that case.

We also added a --reannotate-vcf override argument to explicitly allow reannotation CNV Calling Enabled multi-sample segmentation in ModelSegments Removed mapping error rate from estimate of denoised copy ratios output by gCNV, and updated sklearn. Ran valgrind on limited C unit tests passed Major improvements to input validation Major updates to Error handling and propagation. See This turns out to be more robust in some instances.

To get the new non-standard annotation in HaplotypeCaller you need to add -A AllelePseudoDepth We now track the source of variants in MultiVariantWalkers , which is important for some tools such as VariantEval Bug Fixes Fixed key ordering bugs in the implementations of Histogram.

The Foreign Read Detection FRD model uses an adjusted mapping quality score as well as read strandedness information to penalize reads that are likely to have originated from somewhere else on the genome or from contamination.

Fixed a bug where overlapping reads in subsequent assembly regions could have invalid base qualities Convert non-ACGT IUPAC bases to N in HaplotypeCaller prior to assembly to prevent a crash Renamed the --mapping-quality-threshold argument to --mapping-quality-threshold-for-genotyping , and updated its documentation to be less confusing Added an option for HaplotypeCaller and Mutect2 to produce a bamout without artificial haplotypes Updated the --debug-graph-transformations argument to emit the assembly graph both before and after chain pruning Mutect2 Fixed the --dont-use-soft-clipped-bases argument in Mutect2 to actually work as intended Due to a bug, this option did nothing because a copy of the original reads was modified.

By deleting the unnecessary mapping quality filtering this is totally redundant with the M2 read filter , we finalize and thereby discard soft clips if requested an assembly region made from the original reads, not a copy.

GenomicsDB Introduced a new feature for GenomicsDBImport that allows merging multiple contigs into fewer GenomicsDB partitions Controlled via the new --merge-contigs-into-num-partitions argument to GenomicsDBImport This should produce a huge performance boost in cases where users have a very large number of contigs.

Funcotator Added sorting by strand order for transcript subcomponents This fixes an issue where the coding sequence, protein prediction, and other annotations could be incorrect for the hg19 version of Gencode, due to the individual elements of each transcript appearing in numerical order, rather than the order in which they appear in the transcript at transcription time. Updated the Funcotator tutorial link in the tool documentation. Features to evaluate expression over are defined in an input annotation file in gff3 fomat.

Output is a tsv listing sense and antisense expression for all stranded grouping features, and expression labeled as sense for all unstranded grouping features. ReferenceBlockConcordance : a new tool to evaluate concordance of reference blocks in GVCF files This tool compares the reference blocks of two GVCF files against each other and produces three histograms: Truth block histogram : Indicates the number of occurrences of reference blocks with a given confidence score and length in the truth GVCF Eval block histogram : Indicates the number of occurrences of reference blocks with a given confidence score and length in the eval GVCF Confidence concordance histogram : Reflects the confidence scores of bases in reference blocks in the truth and eval VCF, respectively.

An entry of 10 at bin "80,90" means that there are 10 bases which simultaneously have a reference confidence of 80 in the truth GVCF and a reference confidence of 90 in the eval GVCF.

Updated the GTF versions that are parseable. Fixed a parsing error with new versions of gencode and the remap positions for liftover files.

Added test for indexing new lifted over gencode GTF. Pointed data source downloader at new data sources URL. Minor updates to workflows to point at new data sources. Updated retrieval scripts for dbSNP and Gencode. Added required field to gencode config file generation. Now gencode retrieval script enforces double hash comments at top of gencode GTF files.

Fixed an erroneous trailing tab in MAF file output reported in Added a maximum version number for data sources in Funcotator Added a "requester pays" option to the Funcotator WDL for use with Google Cloud "requester pays" buckets FuncotateSegments : fixed an issue with the default value of --alias-to-key-mapping being set to an immutable value GenomicsDB Updated to GenomicsDB Version 1.

Removed microbial fasta input, as only the sequence dictionary is needed. Broke pipeline down to into smaller tasks. This helps reduce costs by a provisioning fewer resources at the filter and score phases of the pipeline and b reducing job wall time to minimize the likelihood of VM preemption.

Filter-only option, which can be used to cheaply estimate the number of microbial reads in the sample. Metrics are now parsed so they can be fed as output to the Terra data model. This turns on disable file locking and for GenomicsDB import it minimizes writes to disks. The performance on some of the gatk datasets for the import of about 10 samples went from Hopefully this helps with Issue and Also, fixes Issue This version of GenomicsDB also uses pre-compression filters for offset and compression files for new workspaces and genomicsdb arrays.

You can also omit the "--num-executors" argument to enable dynamic allocation if you configure the cluster properly see the Spark website for instructions. Once you're set up, you can run a Spark tool on your Dataproc cluster using a command of the form:. This can be done easily using included gcs-cluster-ui script.

Or see these these instructions for more details. Note that the spark-specific arguments are separated from the tool-specific arguments by a Dataproc Spark clusters are configured with dynamic allocation so you can omit the "--num-executors" argument and let YARN handle it automatically.

Certain GATK tools may optionally generate plots using the R installation provided within the conda environment. If you are uninterested in plotting, R is still required by several of the unit tests. Plotting is currently untested and should be viewed as a convenience rather than a primary output. A tab completion bootstrap file for the bash shell is now included in releases. This file allows the command-line shell to complete GATK run options in a manner equivalent to built-in command-line tools e.

This tab completion functionality has only been tested in the bash shell, and is released as a beta feature. To enable tab completion for the GATK, open a terminal window and source the included tab completion script:. Sourcing this file will allow you to press the tab key twice to get a list of options available to add to your current GATK command. By default you will have to source this file once in each command-line session, then for the rest of the session the GATK tab completion functionality will be available.

GATK tab completion will be available in that current command-line session only. Note that you must have already started typing an invocation of the GATK using gatk for tab completion to initiate:.

Try to keep datafiles under kb in size. GATK4 is Apache 2. TXT file. Do not add any additional license text or accept files with a license included in them. Although we have no specific coverage target, coverage should be extensive enough that if tests pass, the tool is guaranteed to be in a usable state.

All pull requests must be reviewed before merging to master even documentation changes. Don't issue or accept pull requests that introduce warnings.

Warnings must be addressed or suppressed. Don't use toString for anything other than human consumption ie. Don't override clone unless you really know what you're doing. If you do override it, document thoroughly. Otherwise, prefer other means of making copies of objects. For logging, use org. We mostly follow the Google Java Style guide.

If you push to master or mess up the commit history, you owe us 1 growler or tasty snacks at happy hour. If you break the master build, you owe 3 growlers or lots of tasty snacks. Before running the test suite, be sure that you've installed git lfs and downloaded the large test data, following the git lfs setup instructions. To run a subset of tests, use gradle's test filtering see gradle doc :. To run tests and compute coverage reports, run. IntelliJ has a good coverage tool that is preferable for development.

We use Travis-CI as our continuous integration provider. We use Broad Jenkins for our long-running tests and performance tests. We use git-lfs to version and distribute test data that is too large to check into our repository directly. You must install and configure it in order to be able to run our test suite.

After installing git-lfs , run git lfs install. To manually retrieve the large test data, run git lfs pull from the root of your GATK git clone. Ensure that "Gradle project" points to the build. You may need to set this manually after creating the project, to do so find the gradle settings by clicking the wrench icon in the gradle tab on the right bar, from there edit "Gradle JVM" argument to point to Java 1. Set breakpoints, etc. In future debugging sessions, you can simply adjust the "Program Arguments" in the "GATK debug" configuration as needed.

If there are dependency changes in build. This is easily done with the following steps. You must have a registered account on the sonatype JIRA and be approved as a gatk uploader.

If you want to upload a release instead of a snapshot you will additionally need to have access to the gatk signing key and password.

Builds are considered snapshots by default. The archive name is based off of git describe. This has instructions for the Dockerfile in the root directory. To generate the WDL Wrappers, run. To generate WDL Wrappers and validate the resulting outputs, run. If no local install is available, this task will run automatically on travis in a separate job whenever a PR is submitted. Only tools that have been annotated for WDL generation will show up there.

We use Zenhub to organize and track github issues. To add Zenhub to github, go to the Zenhub home page while logged in to github, and click "Add Zenhub to Github". Apache Spark is a fast and general engine for large-scale data processing. In a cluster scenario, your input and output files reside on HDFS, and Spark will run in a distributed fashion on the cluster. The Spark documentation has a good overview of the architecture. Note that if you don't have a dedicated cluster you can run Spark in standalone mode on a single machine, which exercises the distributed code paths, albeit on a single node.

While your Spark job is running, the Spark UI is an excellent place to monitor the progress. Additionally, if you're running tests, then by adding -Dgatk. You can find more information about tuning Spark and choosing good values for important settings such as the number of executors and memory settings at the following:. Note: section inspired by, and some text copied from, Apache Parquet. We welcome all contributions to the GATK project. The contribution can be a issue report or a pull request.

If you're not a committer, you will need to make a fork of the gatk repository and issue a pull request from your fork. For ideas on what to contribute, check issues labeled "Help wanted Community ". Comment on the issue to indicate you're interested in contibuting code and for sharing your questions and ideas.

We tend to do fairly close readings of pull requests, and you may get a lot of comments. Some things to consider:. See also the Contributors list at github. Licensed under the Apache 2. Skip to content. Star 1. Official code repository for GATK versions 4 and up software. View license. Branches Tags.



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