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The GATK Best Practices for variant calling on RNAseq, in full detail
We’re excited to introduce our Best Practices recommendations for calling variants on RNAseq data. These recommendations are based on our classic DNA-focused Best Practices, with some key differences...
View ArticleWhat is the output of MuTect and how should I interpret it?
Please note that this article refers to the original standalone version of MuTect. A new version is now available within GATK (starting at GATK 3.5) under the name MuTect2. This new version is able to...
View ArticleLow coverage loci - GATK pipeline
Hi GATK team, I am posting this question for everyone's benefit as it will shed more light on how HaplotypeCaller and other GATK programs deal with low coverage positions. For the sake of this example,...
View ArticleGATK4 haplotype caller crashes on soft clipped reads at very start of a...
Hi, I am trying out GATK4 Haplotype caller for 8 samples for a non model organism species with a basic reference genome. Output is gVCF. For most of the genome intervals GATK4 Haplotype caller produces...
View ArticleProblem with joint genotyping in gatk 3.7
Hi, When the "GenotypeGVCFs" module in GATK 3.7 is used to generate joint calling it gives either one of these two errors - null pointer exception or a concurrent modification exception. However, on...
View ArticleCan GATK be applied to eCLIP data?
Hi GATK guys, I am now working with eCLIP data with 2 cell lines, each line has multiple (over one hundred) samples. What I need to do is to call variants from each single sample, and combine variant...
View ArticleBQSRPipelineSpark can't run under joinStrategy in SHUFFLE model
I tried to process data with BQSRPipelineSpark( the latest released gatk4 beta version),while it didn't work out unless the data size is small .To illustrate it, we conduct experiments in data...
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...
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Malformed walker argument
Hello, I installed GATK package as explained in the documentation, but I am not able to use the "walkers" with go with it. I always this error message: java -jar GenomeAnalysisTK.jar -T IndelRealigner...
View ArticleTesting different capture reaction template
I did a test of capture sequencing : 96 libraries representing 56 individuals For one individual we made 1,2,3 or 4 libraries. The libraries were pooled before capture reactions so that the same...
View ArticleProblem with GATK pipeline, merging VCF and ped file.
Hi to all I have just started using GATK and I have few question about some tools and about the general workflow. I have 3 exome-seq data from a trio and I have to detect rare or private variants that...
View ArticleGenotypeGVCFs calculateLikelihoodSums NullPointerException
Hi, I run into a NullPointerException exception when trying do use GenotypeGVCFs to merge a set of gVCF files stored via GenomicsDBImport in a database. java.lang.NullPointerException at...
View ArticleDoes IndelRealigner work the same way as the indel realignment included in...
Hello GATK Team, I wonder if IndelRealigner work the same way as the indel realignment included in HaplotypeCaller. Do they use the same algorithm? Does this mean that I don't need to realign indel for...
View ArticleGATK4 beta2 GenotypeGVCFs produces VCF with no records, just a header
Hi, GATK4 beta2 GenotypeGVCFs produces a VCF with no records on my test data. The file does contain a valid VCF header. The commands that I used for GenomicsDBImport and GenotypeGVCFs are below. Both...
View Articleoverlap between mutect and mutect2
I am running mutect 1.1.7 and mutect2 (GATK 3.7) on tumor/normal paired samples and compare results between the two, the overlap are usually very good at ~90%. But I got poor overlap ( <20%) for a...
View ArticleProblem with HaplotypeCaller and GenotypeGVCFs
Hi just wondering if you have any experience with this problem. I am following GATK best practices for a targeted sequencing experiment. After the GenotypeGVCFs phase the majority of variants are...
View ArticleRealignerTargetCreator hangs
Hi GATK team! we have an issue with running the RealignerTargetCreator unfortunately. Commandline looks like this: gatk -T RealignerTargetCreator -R ref.fasta -I /testsample.sorted.bam -nt 32 -o...
View ArticleRequire Genotypes in VCF file in order to output Fst statistics
Hello, I am using a VCF file obtained from "GenotypeGVCFs" to calculate Fst statistics with VCF tools. I get this error message: Error: Require Genotypes in VCF file in order to output Fst statistics....
View Article(howto) 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...
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