HaplotypeCaller non-descript error
Hello all, I'm trying to run HaplotypeCaller on a bam that I've created following the Best Practices, however it fails and gives me the following error message: ERROR...
View ArticleDifference in GenotypeConcordance between GATK and Picard tools
Hi, I am trying to compare Genotype calls between two multi-sample VCFs. I ran the GenotypeConcordance tools from both GATK and Picard (Picard version for just one of the samples). But I see that the...
View ArticleHaplotypeCaller: Alleles for a VariantContext must contain at least one...
Howdy. I'm playing with the 7-12 nightly to fix the HashMap iterator issue in http://gatkforums.broadinstitute.org/gatk/discussion/comment/30982#Comment_30982 When running HaplotypeCaller however, I...
View ArticleGenomestrip CNV results wonky
Hi @bhandsaker The results of CNVdiscovery followed by compute allele frequencies, are a bit weird for me. I've attached two IGV images, showing both the genomestrip vcf file, and bam files from two of...
View ArticleSetting up your dev environment: Maven and IntelliJ for GATK 3+
Overview Since GATK 3.0, we use Apache Maven (instead of Ant) as our build system, and IntelliJ as our IDE (Integrated Development Environment). This document describes how to get set up to use Maven...
View ArticleBaseRecalibrator/PrinReads - fatal error
Hi the team, I have a "random" issue with the base recalibration step of my pipeline, occuring at the PrintReads step more precisely. The command lines follow this pattern : java -jar -Xmx4g...
View ArticleFailed to annotate InbreedingCoeff
Dear GATK team, I'm working on the VQSR step, and the inbreedingcoeff given as recommend annotation. Since it can only be annotated when there are >10 samples, so I merged my 35 samples' MuTect2...
View Articlefastq files of whole exome sequencing (WES) of somatic mutations
Hi all, I am looking for raw data (fastq files) of whole exome sequencing (WES) of somatic mutations to benchmark my GATK-MuTect pipeline. Do you know where can I find publicly available samples for...
View Article(howto) Install and run Oncotator for the first time
1. Download the Oncotator package, the default datasources package, and (recommended) transcript override list from the Downloads page Please note: Broadies who wish to run the installed Oncotator on...
View ArticleHow to get GATK 3.5?
The current version of GATK is 3.6-0 I can not find v3.5 in archived versions. Could you add the access to v3.5?
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Genotype Refinement workflow
Overview This document describes the purpose and general principles of the Genotype Refinement workflow. For the mathematical details of the methods involved, please see the Genotype Refinement math...
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[How to] Generate a BAM for variant discovery (long)
[work in progress--I am breaking this up into smaller chunks] This document in part replaces the previous post (howto) Revert a BAM file to FastQ format that uses HTSlib commands. The workflow assumes...
View Article(howto) Apply hard filters to a call set
Objective Apply hard filters to a variant callset that is too small for VQSR or for which truth/training sets are not available. Caveat This document is intended to illustrate how to compose and run...
View ArticlePicard MergeVcfs vs GATK CatVariants
I've noticed the WDL scripts are using Picard's MergeVcfs immediately following a scattered GATK HaplotypeCaller to do what CatVariants was seemingly designed for. Is there any benefit to using one...
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Can't compile GATK 3.6 from source
Hi there, I'm trying to compile GATK 3.6 from source and it ain't working out for me Here is my system specs, also showing there that I got master branch clone that I'm trying to complie...
View ArticleHow can I turn off or decrease downsampling in MuTect2?
According to MuTect2s docs, the default is to downsample by sample to 1,000x. I would like to lower this substantially to something like 3,000 or lower. When I use the -dcov argument in my command line...
View ArticleDifferent ARO with or without -justDetermineActiveRegions for HaplotypeCaller
I noticed that for one BAM, when calling HaplotypeCaller (I am using version 3.5), with or without the -justDetermineActiveRegions, the ARO results are different at several intervals. For example, one...
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 ArticleMutect version of Picard tool for filtering
Hello All, I am using Mutect for variant discovery on RNA-seq data and I am following Best practices, but I didn't see a direct description about which version of Picard should used for reordering and...
View ArticleMutect1.1.7 clustered position filter for soft-clipped reads
Hello, Please can you consult me. I have an example of a candidate somatic variant where all variant reads are soft-clipped (3 bases from the mutation). The variant is naturally rejected by Mutect when...
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