GenotypeGVCFs (V4.0) memory error
Hi all, I recently upgraded to GATK 4, and have been having problems with GenotypeGVCFs. I noticed that this problem only occurs as I introduced more samples. I also noticed that other uses have been...
View ArticleAmbiguous error in GenomicDBImport
Hi, in the HaplotypeCaller step I use 404 intervals with 100bp padding. Then, when I'm going to create the DB wiht GenomicDBImport , with the same range of intervals, only in some in some cases I have...
View Articlecombine GVCFs error
I am trying to combine 240 gvcf files to run joint GenotypeGVCFs. I created 12 meta-merged-GVCFs by combining 20 samples into one.and I did this separately for each chromosome. When I combine 12...
View ArticleInbreedingCoeff in VCF not matching my calculation
Initially I was going to ask about why I might be seeing some InbreedingCoeff values less than -1 (based on the calculation as explained at...
View ArticleWhy is converting from fastq to uBAM nesessary before preprocessing?
Hi Everyone, I am brand new to this so please go easy on me. I have just taken over a project where we are going to be doing variant calling on a large number of human samples. I have inherited a...
View ArticleException Running CombineGVCFs
I am running CombineGVCFs on single sample gvcf files produced by Haplotype caller. "java.lang.IllegalStateException: Key END found in VariantContext field INFO at NC_002971.4:6584 but this key isn't...
View ArticleWhy does GenotypeGVCFs with and without the "includeNonVariantSites" option...
Hi GATK team, For reasons explained in another discussion (https://gatkforums.broadinstitute.org/gatk/discussion/10751/high-proportion-of-spanning-deletion-in-a-whole-genome-callset#latest) we decided...
View ArticleBuild Error in Mutect: GATK-Framework
Hi everyone, I am trying to install mutect on a Mac (El Capitan). The command mvn -Ddisable.queue install Is throwing this error message and I'd need you help here. [INFO] 5 warnings [INFO]...
View Article[WDL][Cromwell[ Mounting a directory to the docker for access.
Hi, I am attempting to run Gemini within a docker through WDL and Cromwell. I have installed gemini with no data as the data is too large to be put into a Docker (plus it's bad practice). So I need to...
View ArticleCalculateContamination output table
The CalculateContamination description says: Calculates the fraction of reads coming from cross-sample contamination, given results from GetPileupSummaries ... this tool estimates contamination based...
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 ArticleVCF file and allele frequency
Hello All, I am using I am using GATK RNA-seq variant pipeline for finding muttaion/vatiants on the list of gene given in teh follwoing command line java-1.7 -jar -Xincgc -Xmx1586M...
View ArticleGenomeAnalysisTK Mutect2 Error...
Dear All, I used samtools-0.1.19 got the alignment bam file and index, then I am going to use GenomeAnalysisTK/3.5/java.1.7.0_67 to call variations, but it is not working. If someone can give any...
View ArticleMeaning of "overlapping" in CollectHsMetrics option CLIP_OVERLAPPING_READS
I had originally interpreted the meaning of "overlapping" in CollectHsMetrics option CLIP_OVERLAPPING_READS as applying to reads that overlap a target interval but extend past the end of the interval...
View ArticleBatch options in GenomicsDBImport
Hi, We are planning to test around 5000 WGS samples for Joint Variant calling and would like to follow as mentioned here https://software.broadinstitute.org/gatk/documentation/article?id=10061 One of...
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Why GATK 3.7 VariantAnnotator - Processed 0 loci
I was trying to use GATK 3.7 VariantAnnotator to annotate a vcf.gz file. Here is my code: /u/local/apps/java/jdk1.8.0_111/bin/java -jar /u/local/apps/gatk/3.7/GenomeAnalysisTK.jar \ -T...
View ArticleGATK3.8 vs GATK4 HaplotypeCaller
Hello, maybe I'm asking a naive question and maybe it has been answered somewhere else, but as the title states are there differences in the algorithm of the HaplotypeCaller between GATK3.8 release and...
View ArticleTruncated Bam error in recalibrated bam file
I am trying to complete my pipeline to get variant calls and annotation using various tools of gatk. I am getting stuck in last step of post-processing. Here is my post-processing steps: Sam-to-Bam...
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(How to) Map reads to a reference with alternate contigs like GRCh38
Document is in BETA. It may be incomplete and/or inaccurate. Post suggestions to the Comments section and be sure to read about updates also within the Comments section. This exploratory tutorial...
View ArticleRADseq data and GATK
Hello! I am pretty new to bioinformatics- mostly just have taken one class. I have been handed some RADseq data and we want to do some SNP variant calling. I am trying to make sure that I use GATK...
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