Variants in pseudogene or repeat region
Hi all, We used PCR to enrich the target amplicon, and get sequenced on HiSeq X. In our targets, several are located in pseudogenes or repeat region. We used bwa mem to align the reads to genome with...
View ArticleIssue with reassembly (potentially) in HaplotypeCaller
I have a question about how the reassembly works in HaplotypeCaller from GATK version 3.6-0-g89b7209. I have been checking the SNPs called in IGV and I have found a couple of regions that very clearly...
View ArticleBest practices for calling variants in RNAseq data
Dear GATK team, Is there any link with detailed best practices for calling variants in RNAseq data? Thanks
View ArticleMutect2 with contamination estimates
Hi GATK How many sites does ContEst need to get an accurate answer? A couple of my samples give me results like this: name population population_fit contamination confidence_interval_95_width...
View ArticleHow to make MergeBamAlignment work?
Hi guys, I think I am missing something with this process (obviously...): Using latest version of Picard Tools. Reads are Illumina 100bp single end. Pre-processing includes de-multiplexing, FastQC and...
View ArticleMalformedWalkerArgumentsException?
I'm trying to run GATK integration tests locally on a custom walker. This was working fine for a few days. This afternoon, inexplicably, one of the integration tests began to fail with a...
View Articledepth of coverage from gVCF files
Dear all, I have a large number of gVCF files, either single samples or combined in approximately 100 samples per combined gVCF file. I would like to compute something like the average depth for a set...
View Articlehow to determine whether the variants is true by the IGV alignment views ?
Hi, how to determine whether the variants is true by the IGV alignment views ? is there a good paper to introduce that ? Best
View ArticleWhat do GATK workshops cover?
This is the description of our current 3-day workshop formula. 3-Day workshop summary This workshop will focus on the core steps involved in calling variants with the Broadās Genome Analysis Toolkit,...
View ArticleRun time error with VariantsToBinaryPed
Hi, I am trying to covert a vcf file to a bed file using VariantsToBinaryPed. Input: vcf file and metadata file. Error below. Can anyone advise? Thanks! [umcv@node021 unag]$ java -jar...
View Article(howto) Test your GATK installation
Objective Test that the GATK is correctly installed, and that the supporting tools like Java are in your path. Prerequisites Basic familiarity with the command-line environment Understand what is a...
View ArticleTop Reasons To Move From LAMP To MEAN STACK For Web Development
Stacking web technologies is a common phenomenon adopted by developers since years to gain prominence in website development. One of the earliest web stacks formed with well-known open source...
View ArticleMutect2 vcf FORMAT field
Hi, Iām trying to use Mutect2 (GATK version 3.7) for somatic mutation calling. I noticed that if I use it with the default parameters in the FORMAT field I have the following informations:...
View ArticleAC,AF, and AN INFO fields are not defined in output from HaplotypeCaller
Hi, I have a problem where the output vcf from the haplotypecaller doesn't include meta-information lines for the AC,AF, and AN info fields, yet one of the records in the vcf contains these info...
View ArticleCall Varients from RNA-seq for RNA editing detection
Dear GATK staff I would like to use the GATK tool for the detection of possible RNA editing events. I followed the RNA-seq best practice up to the variant calling step itself. There I hesitate to use...
View ArticleDescription and examples of the steps in the CNV case and CNV PoN creation...
The CNV case and PoN workflows (description and examples) for earlier releases of GATK4. For a newer tutorial using GATK4's v1.0.0.0-alpha1.2.3 release (Version:0288cff-SNAPSHOT from September 2016),...
View ArticleWhat does the output of DepthOfCoverage means?
I have tried looking for the good discussion on how to calculate the average coverage of exome sequencing after alignment. I found that depthofcoverage is a good tool to get the output, however, I am...
View ArticleArbitrary sorting of inputs in method configuration?
I'm configuring my new method called DellyForGermlineSV in the broad-firecloud-dsde-methods/CCDG-500-testForManta workspace. The inputs are listed in some order than isn't the order in my WDL and isn't...
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Unboxing GATK4
This is one of two posts announcing the imminent beta release of GATK4; for details about the open-source licensing, see this other post. You've probably heard it by now: we are on the cusp of...
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GATK4 is completely open source
This is one of two posts announcing the imminent beta release of GATK4; for a technical description of features, see this other post. "Wait, what?" Yes, you read that right, we're moving GATK4 to a...
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