What is the best way to find denovo mutations in trios?
I have around 100 trios for which WES was done. My goal is to find denovo mutations in the child associated with each trios. So first I will do the following steps: 1 -Alignment to reference genome 2 -...
View ArticleProblem with joint genotyping
Dear Team, I am running joint calling (according to Best Practices). I have ~800 samples from 3 different centres.First I run CombineGVCFs on cases from batch1(~130samples), controls from...
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What is a VCF and how should I interpret it?
This document describes "regular" VCF files produced for GERMLINE calls. For information on the special kind of VCF called gVCF, produced by HaplotypeCaller in -ERC GVCF mode, please see this companion...
View ArticleProblem with LiftoverVcf
It is my first time running the LiftoverVcf, but I saw that many other users passed through difficulties similar to mine but not exactly the same. I'm trying to convert a vcf file from Hg18 to Hh19....
View ArticleError trying to use MuTect2
Hi, I've seen posts with similar questions about this error, but the solutions didn't seem to help me/I may not have understood them entirely. I'm running Java version 9.0.1 and downloaded the GATK...
View ArticlePresentation slides and tutorial materials - Pretoria 2017
The presentation slide decks and hands-on tutorial materials presented at the 5-day GATK workshop in Pretoria, South Africa can be downloaded at this Google Drive link.
View ArticlePicard CheckIlluminaDirectory Failing
Hello, I have a MiSeq run that I wish to run ExtractIlluminaBarcodes and IlluminaBasecallsToSam on, however, they can't find the files needed. When I run CheckIlluminaDiretcory I get this result...
View ArticleGATK depth of coverage
I am calculating the Depth of coverage for 100 samples using the following command java -Xmx20g -XX:ParallelGCThreads=20 -jar /mnt/exome/Softwares/GenomeAnalysisTK.jar -T DepthOfCoverage -I BAMaa.list...
View ArticleHappy New Year 2015 and welcome back to the GATK forum
It's a shiny New Year and the forum, like the rest of Broad, is back to active status, so bring it on! It might take us a day or two to mop up the questions that came in during the break so we...
View ArticleUnifiedGenotyper takes too long to init with big reference
Hello, I'm using GATK version 3.7-0-gcfedb67 in a Linux 3.13.0-93-generic x86_64 with 64 CPUs UnifiedGenotyper is taking way to long to run with a large, fragmented fragmented reference (>300,000...
View ArticleDangling heads and tails
Hello, The logic for merging dangling tails appears to be different from that for dangling heads. For example, it looks like tails can be merged to a non-reference path while heads cannot. Is there a...
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Mutect 2 java memory shortage: a case study.
Hi all, I've recently been finding memory problems when running GATK3 Mutect2. I know updating to GATK4 might resolve some of the problems, but let's say for educational purposes that that is not an...
View ArticleNew to GenomeSTRiP - Running Installtest Properly
So i am new to GenomeSTRiP. I have downloaded and extracted all the necessary pieces to run it and tried running the installtest. I ran the install test twice using two different commands, the first...
View ArticleOpen Tumor / Normal pair dataset for benchmarking and training
Hi, I am looking for a real tumor normal pair dataset to apply analysis and compare callers. Do you know of one I can get (bam would be quicker but even fastq is OK as I could map against 38 to be...
View ArticleJEXL filtering using criteria for groups of individuals instead of all single?
I have used JEXL-filtering to specify variable criteria for each normal in a cohort of control sample (for comparison to affected samples), like " -select ' vc.getGenotype("Normal1").isHomRef()...
View ArticleAllele balance filtering
I am getting a number of incorrect/questionable genotype calls after proceeding through the "Best Practices" guidelines. These incorrect calls are resulting in a lot of false positives in my subsequent...
View ArticleWhat causes BaseRecalibratorSpark to run for a long time and end up failing...
Hi, GATK team, I am testing BaseRecalibrator in GATK 4.5 beta, when running in LOCAL mode, it finishes pretty fast. However when i run BaseRecalibratorSpark in SPARK mode, it runs for a long time and...
View ArticleGetBayesianHetCoverage exits with code 247
When I run GetBayesianHetCoverage in a Docker container, the function exits without completing with code 247. The Docker container is built from an image that uses the Debian "Stretch" base image, with...
View ArticleInvolving the svtoolkit/cookbook/.../set_sv_params.sh
I am running through the cookbook example given found at: http://software.broadinstitute.org/software/genomestrip/cookbook-genotyping-novel-site-1000-genomes-phase-1 The set_sv_params.sh file needs to...
View ArticleQuestions about the RNAseq variant discovery workflow
This discussion was created from comments split from: Calling variants in RNAseq.
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