Oncotator Error -- Please help me
I am running Oncotator 1.8.0.0 on MuTect2 output .vcf file. I did perform filtering for PASS before running Oncotator. If I run this on command line: oncotator -v --input_format=VCF --output_format=VCF...
View ArticleCannot Download GATK 3.7-0
Dear GATK Team, It may be so silly, but, I can't download current version of GATK. It persist in the message "You must be logged into the forums to proceed. You do not seem to be logged into the...
View ArticleI have recently registered but I have problems accessing the GATK downloads.
I have recently registered for an account at the GATK-forum. I have problems accessing the downloads. When I try to download, I am taken back to the window to login even when I am already logged in. I...
View ArticleIs 70k millions variants for WES trios enough?
Hi there, I am using GATK for trio analysis of WES data where I have proband and parents. I would like to execute a Joint analysis of all the 50 families that I have but could not get more than about...
View ArticleHaplotypeCaller in GATK4 vs GATK3
I know that HaplotypeCaller in GATK4 is still in development, but I want to make sure this issue is known We're seeing very different behaviour between the HC in GATK3 and GATK4 when using targeted...
View Articlewhy I can not download GATK?
Hi, I've tried to download GATK program but I can't ...does anyone know what is going on? Thanks!
View ArticleBest practices for calling variants in RNA-seq data
Dear GATK team, Is there any link where I can find details about calling variants from RNA-seq data? Thanks
View ArticleUnable to run JAR from GitHub
Hi, I've tried to download GATK-3.7 from https://github.com/broadgsa/gatk/releases as follow 1) downloaded tar.gz 2) tar xvzf gatk-3.7.tar.gz (linux comand) 3)Inside the folder there are lot of folders...
View Article[GATK 4 beta] Allele in genotype T not in the variant context exception in...
Hello, It looks that FilterByOrientationBias tool gives the following exception: java.lang.IllegalStateException: Allele in genotype T not in the variant context [G*, A] Would you give any advise on...
View ArticleGATK4 annotation error
when I use gatk4 Haplotypecaller with -A option,a error was appear. A USER ERROR has occurred: Argument annotation has a bad value: Annotation [AlleleBalance, HomopolymerRun, GCContent, LowMQ] not...
View ArticleCalculateGenotypePosteriors (hg19) error
Hi, I converted 1000G_phase3_v4_20130502.sites.vcf to hg19 using Picard 2.10.0 with the following command: java -Xincgc -Xmx5G -jar /data/home/hhx037/picard-tools/picard.jar LiftoverVcf...
View ArticleCalculateContamination output format
The docs of CalculateContamination says the output is The resulting table provides the fraction contamination, one line per sample, e.g. SampleID--TAB--Contamination. The file has no header. But here...
View Article[GATK 4 beta] GermlineCNVCaller for trio
Hi, There are LEARN_AND_CALL and CALL_ONLY two modes in GermlineCNVCaller. Could I use GermlineCNVCaller for trio analysis?
View Article[GATK4-beta1 problem]Some questions about BWA/FAGA/pipeline in GATK4-beta1
We use GATK4-beta1 in ARM,and have several questions about it: 1. When I run BwaMemIndexImageCreator, it has error which is "We have pre-built fermi-lite binaries only for x86_64 and amd64. Your...
View Articlewhat's the difference between mutect and GATK-Mutect ?
HI, I do not know the difference between the mutect from http://archive.broadinstitute.org/cancer/cga/mutect and from GATK ? I find the latest version is 1.14 at the CGA...
View ArticleDownload previous versions
I apologize, but I can not find relevant threads regarding if I can download previous builds of GATK. Perhaps I am not using the proper search tags. I would like to specifically get version 2.5-9 to...
View Articlegenerate an idx file for a vcf
Hello, I have a vcf file that does not have an associated index file. Is it possible to create one? If yes, what module do I need to use? Thanks for your input! ~Mika.
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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 ArticleCOSMIC and dbSNP files for MuTect
I'm having trouble finding the recommended COSMIC and dbSNP file for hg19 to use with MuTect (hg19_cosmic_v54_120711.vcf and dbsnp_132_b37.leftAligned.vcf). I can't find these in any of the bundles on...
View ArticleWhy I can not reproduce my result on different hostcomputer?
Dear colleague, I have encounter a strange issues with GATK-3.3/3.7: I used HaplotypeCaller to call variants on the same realn.recal.bam file, and it gave me different results when i ran on different...
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