Reasons MarkDuplicates might not remove all duplicates?
I was using MarkDuplicates to remove duplicates from a BAM file with extremely high coverage. It was for the gene GAPDH, and I calculated the maximum possible number of bases using Ensembl BioMart to...
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 Articlehow to view points distribution and genes across the whole human genome from...
HI, I have a bed file , then I wanna konw how to view points distribution across the whole genome from the bed file ,and also mark genes . my bed format just like this : chr start end...
View ArticleGATK 4
Hi,Is there any sort of estimated timeframe for GATK 4 to be officially released (i.e. a non-beta release)?Thanks!
View Articlepicard of CollectVariantCallingMetrics error
[Thu Jun 29 17:13:02 CST 2017] picard.vcf.CollectVariantCallingMetrics INPUT=BGIyaozu.qc.vcf OUTPUT=BGIyaozu DBSNP=dbsnp_138.hg19.vcf GVCF_INPUT=false THREAD_COUNT=1 VERBOSITY=INFO QUIET=false...
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 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 ArticleGATK4-Alpha MarkDuplicates crashing
I've used Picard2.1 MarkDuplicates for a bunch of bam files (4-40x coverage) generated with Picard2.1 MergeSamFiles and it works fine. I'm trying to get GATK4-Alpha MarkDuplicates working on the same...
View ArticleWhat do I need to do before attending a workshop hands-on session?
So you're going to a GATK workshop, and you've been selected to participate in a hands-on session? Fantastic! We're looking forward to walking you through some exercises that will help you master the...
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 ArticleJar caching and enabling it
When running GATK4 Spark jobs, we see in the standard output a message about caching the jar file. Using GATK jar /Applications/genomicstools/gatk/gatk-4.latest/gatk-package-4.beta.2-spark.jar jar...
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 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 Articlepicard 2.10.7 fails pipelining SortSam and SetNmAndUqTags
Hi. I just upgraded to picard 2.10.7 and doing my regular exome work however I noticed this problem under 2 different platforms. 18:12:17.734 INFO NativeLibraryLoader - Loading libgkl_compression.dylib...
View ArticleClik here to view.
(How to) Run FlagStatSpark on a cloud Spark cluster
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 tutorial outlines the most...
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 Article