Large Batch - "Unable to create BasicFeatureReader"
Hi, I've been running into an error using GATK 3.8-0, " Unable to create BasicFeatureReader using feature file , for input source: " when I try to do a somewhat-large batch call of bgzipped and tabix...
View ArticleHow can I get a common variant of three samples from multi-sample VCF after...
Hi. I’m studying about sequencing data analysis followed GATK Best practices for Germline SNP & Indel Discovery. Through the series of analysis, finally I get multi-sample VCF file from joint...
View ArticleQuestions about BQSR (2014-2016)
This discussion was created from comments split from: Base Quality Score Recalibration (BQSR).
View ArticleWell-calibrated likelihood that a variant is truly heterozygous rather than...
Hi, I have whole genome sequencing data, and I am trying to assemble a list of sites which are heterozygous with high confidence. VariantRecalibrator seems to estimate two distributions: a (0/0)...
View ArticleCalculateGenotypePosteriors error
Hi, I've run the GATK best practices pipeline up through VQSR and have the recalibrated variants in a VCF file. Because I'm analyzing pedigree samples, I'm now attempting to run...
View Article(howto) Run the genotype refinement workflow
Overview This tutorial describes step-by-step instruction for applying the Genotype Refinement workflow (described in this method article) to your data. Step 1: Derive posterior probabilities of...
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 ArticleCombineVariants fail when combining vcf from genotypeGVCFs genotyped using...
When I attempt to run the tools CombineVariant with two vcf files generated from GenotypeGVCFs using the flag -allSites I get an error saying that I should not use combineVariants in a gvcf file. But...
View ArticleHow can I use parallelism to make GATK tools run faster?
This document provides technical details and recommendations on how the parallelism options offered by the GATK can be used to yield optimal performance results. Overview As explained in the primer on...
View ArticleMy VQSR tranches-plot shows cumulative variants in tranch 0-90, 90-99, 99-99.9
Dear GATK-Team, My VQSR tranches-plot (exome data) shows cumulative variants in tranch 0-90, 90-99, 99-99.9. To my understanding it should be the other way round (like in your article link). My tranch...
View ArticleUsage of "--dontUseSoftClippedBases" HaplotypeCaller option for exom...
Hi GATK Team, HaplotypeCaller does not call structural variants from soft clipped bases, therefore the "--dontUseSoftClippedBases" should mainly reduce false positives (e.g. incomplete adapter...
View ArticleForum Search Problem
Hi there, I appear to be unable to navigate to pages beyond page 1 in search results on the forum site. The page navigation numbers near the bottom of the search results page appear to not be...
View ArticleTruth & Control sources- HapMap and 1000G
Hi everyone, I apologize in advance if this question seems like a stupid one, but I have always thought that sources such as HapMap and 1000G from the resource bundle that we use in VQSR are comprised...
View ArticlemuTect2: ": Somehow the requested coordinate is not covered by the read. Too...
Hello! I am using muTect2 (in particular I am following this pipeline: http://gatkforums.broadinstitute.org/gatk/discussion/5963/tumor-normal-paired-exome-sequencing-pipeline) but today I am getting...
View Articlejava.lang.RuntimeException: Error processing input from file.bam: Invalid...
I'm getting the error above when I run Genome Strip discovery pipeline. I would appreciate help troubleshooting. Below are the lines in the output beginning with the first error through the end of the...
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热烈欢迎我们的中国朋友 / A warm welcome to our Chinese friends
科研圈的亲们，我们来啦！携手国内重量级公司和机构，我们这次给大家带来了高效、规模化使用GATK的技巧！ Today we are reaching out to the Chinese research community with great news: we are partnering with key companies and institutions in China to...
View Articlethe point of Co-realign in indel realignment?
GATK RealignerTargetCreator 's input is a normal-tumor bam list,is there any difference in output with put the bam files one by one?why need the co-realign,why not just realignment one by one?
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(How to) Run the GATK4 Docker locally and take a look inside
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. 1. Install Docker on your...
View ArticleGATK 4.beta.2 vs. 4.beta.3 performance
Hi, I've been keeping up with the GATK 4.0 beta releases and I've noticed some performance differences between my runs of version 4.beta.2 and 4.beta.3. That is, 4.beta.3 tools seem to have a longer...
View ArticleWhat is this error? and how to resolve it? It is related to generating pdf
INFO 13:15:42,730 AnalyzeCovariates - Generating plots file 'LB0003_recal_plots.pdf' ERROR -- ERROR stack trace org.broadinstitute.gatk.utils.R.RScriptExecutorException: RScript exited with 1. Run with...
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