Large vcf files after running the GATK SNV + indel pipeline
Hi Simple question: Why do I get large vcf files after filtering variant calls? I am following your best practice pipeline (SNV + indel), with some minor modifications suggested in another thread (with...
View ArticleGot error of java.lang.IllegalArgumentException: Invalid interval. Contig:81...
I have run 96 samples with somatic short variant calling pipeline with GATK version (gatk-4.1.4.0) and only three of them have this problem :java.lang.IllegalArgumentException: Invalid interval....
View ArticleHow to identify duplicated genes in VCF file obtained after GATK pipeline?
I am working to find which gene type is more duplicated. I had mapped and annotated my VCF file by GATK pipeline. Please guide me how to proceed now.
View ArticleMasking Polymorphic Regions Before Variant Calling
I notice that the best practices workflows treat all regions in the reference genome the same. A region such as the MHC region containing the HLA genes is extremely polymorphic. There are thousands of...
View ArticleMergeBamAlignment – Select primary alignment
Hi, In the current best practices workflow gatk4-data-processing, you recommend using uBAMs instead of FASTQ files. Great idea! However, when it comes to merging with the BWA alignment BAM, there is...
View ArticleAlternative resources for Mutect2/GetPileupSummaries when dealing with genome...
Hi I'm currently using GATK 4.1.2.0, following the best practices for somatic variant calling. I already have this set up for exomes, but I'm now attempting to run the same pipeline on genome data. I'm...
View ArticleError running GenomicsDBImport in parallel (java.lang.UnsatisfiedLinkError:...
Hi, I am using the scatter gather approach to run the Germline short variant discovery workflow. I am using GenomicsDBImport to consolidate GVCFs per scatter interval to allow joint genotyping with...
View ArticleDifferent resource for Mutect2/GetPileupSummaries when dealing with genome data
Hi, Firstly, could someone please set the category for this question to the most relevant? For some reason it's only letting me select Zoo & Garden from the menu. I'm currently using GATK 4.1.2.0,...
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Missing variants using the GATK best practices.
Hi, I am working with human whole exome (WES - Illumina, paired end) data and trying to perform variant calling by following the GATK best practices with GATK v4.1.2.0 installation(I know that there...
View ArticlePipeline Index
This document is under construction. It aims to provide an overview of use cases covered by GATK Best Practices workflows. Variant Discovery Germline Somatic Notes Data pre-processing Single-sample...
View ArticleBWA and fastqtosam failing with read names do not match errors
I'm using the GATK best practices to call public exome data. Out of over 600 exomes, most of the samples did fine with BWA mem alignment and fastqtosam. About 100 samples failed both steps (the same...
View Articlewhy variant callers's (GATK3.8 and GATK 4.0) results are different ?
hello, i am beginner . i used two different tools to analyze my data but i got the two different why ?
View ArticleWDL + Cromwell + AWS Batch
Hi all - I'm trying to figure out the best way to write pipelines in WDL with AWS Batch. As I understand it, each Task in WDL is a separate AWS Batch job. As such, each Batch job can run on any...
View ArticleError with GenomicsDBImport input file
Hi, I am trying to run GenomicsDBImport to test my pipeline with just 2 samples. I am using the following code: gatk GenomicsDBImport \ -V $SCRATCH/active/memtest2/ SRR112728.raw.snps.indels.g.vcf \ -V...
View ArticleIntroduction to the GATK Best Practices workflows
This article is part of the Best Practices documentation. See http://www.broadinstitute.org/gatk/guide/best-practices for the full documentation set. The "GATK Best Practices" are workflow descriptions...
View ArticleGATK4 best practices error
with respect to the gatk best practice [manual]: https://software.broadinstitute.org/gatk/best-practices/workflow?id=11165. Mark Duplicates section:- which reads MarkDuplicates to perform the duplicate...
View ArticleGermlineCNVCaller parameters for targeted sequencing
Hi all, I am testing the presence of CNVs on target sequencing data related to a gene panel of ~100 genes. I have seen in the forum and from various posts that some of the parameters changes between...
View ArticleHow to set GVCF genotypes too ./. based on the GQ score
Hi, I have a reasonably large non-human multi-VCF dataset containing ~280 samples and ~70M variants. I want to filter low quality genotype calls (but not variants as a whole). This does not seem to be...
View ArticleGATK usage for Targetted Exome sequencing data analysis
We are using a licensed version of GATK here. The version is GATK version -2014.3-3.2.2-7-g f9cba99. While using the tool for analysis of exome data I had few questions. 1: Are there different...
View ArticleThe stop position is less than start for Broad.human.exome.b37.scattered.txt
I was running a test with the the gatk3 germline workflow (located at `gatk-workflows/gatk3-germline-snps-indels` on GitHub), but since I'm only interested in exome performance I used the...
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