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java.lang.IncompatibleClassChangeError GATK 4
Hi, I hit an error with GATK 4 beta 6 using the RealignerTargetCreator - as a complete java newbie it's quite incomprehensible to me. I'm running (oracle) java 9.0.1(and thus GATK 3...
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GATK reported a deletion as a homozygous while the same deletion is shown...
I am using GATK version 3.7 and following best practice pipeline as recommended for cohorts analysis. I have called variants using HaplotypeCaller joint genotyping with default parameters from 70...
View ArticleMuTect2 beta --germline_resource for build b37
Hi - I'm looking to run MuTect2 beta using the --germline_resource option. However, I've consistently used the b37 genome build throughout my analaysis, while the suggested resource (gnomad) appears to...
View Article1000G.phase3.integrated.sites_only.no_MATCHED_REV.hg38.vcf corrupted?
Hi i downloaded the file from GATK google cloud but it seems the file is corrupted? only chr1-chr15 sites are present.
View ArticleLiftoverVcf no output
Hi! I'm using LiftoverVcf to make a hg38 version of the gnomad file from the GATK resource bundle The gnomad file is in b37 version, as there isn't a chain file for b37 -> hg38, I have to do b37...
View Articledetect MNP variants using by Haplotypecaller
Hi! I used Haplotypecaller 3.1 to detect MNP variants. java -Xmx6g -Djava.io.tmpdir=$PWD -jar $GATK -R $hg19 -T HaplotypeCaller -I $bamlist --dbsnp $dpsnp135 -o $call/$sample.all.vcf -stand_call_conf...
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Why is HaplotypeCaller slower in the most recent GATK4 beta versions?
Because it's saving its strength for the 4.0 general release Many of the "early adopters" who have been testing out the GATK4 during its beta phase have pointed out that they saw significant speed...
View ArticleVariant annotations
Variant annotations are available to HaplotypeCaller, Mutect2, VariantAnnotator and GenotypeGVCFs. These are listed under Annotations in the Tool Documentation. HaplotypeCaller and Mutect2 calculate...
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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 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 ArticleGATK4-beta Mutect2 input and samplenames
I'm using paired tumor-normal samples, and since the command line parameters have changes, I wanted to make sure that I'm defining my input files and sample names correctly. The command I use is java...
View ArticleHow to define different target regions in Haplotypecaller?
Hi, I'm new to use GATK to analyze whole-exome sequencing. I'm wondering how to define different target regions in HaplotypeCaller for the label (-L). The customer provides me a bed file. Your help...
View Articlehelp with picard CollectHsMetrics
I tried to run CollectHsMetrics with this command java -jar /picard.jar CollectHsMetrics \ I=190.sortedDeDup.bam \ O=190_hs_metrics.txt \ R=ucsc.hg19.fasta \...
View ArticleHow MuTect filters candidate mutations
Please note that this article refers to the original standalone version of MuTect. A new version is now available within GATK (starting at GATK 3.5) under the name MuTect2. This new version is able to...
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[GATK 4 beta] clustered_events in Mutect2/FilterMutectCalls
Hi, I have a question about filtering Mutect2 calls. A well-characterized SNV (vcf records below 17:7577120) is filtered out by clustered_events filter. It appears that an artificial haplotype is...
View ArticleIs the GATK resource bundle data outdated?
The version of dbSNP at the research bundle is 138 for hg19 (updated 8.12.2013), but the latest dbSNP version is 150:...
View ArticleVariantAnnotator using GnomAD gives NullPointerException
Hello, Running VariantAnnotator, I am running into errors I couldn't find solutions for in the forum. Using the GnomAD publicly available VCF's, I would like to add information to a VCF, specifically...
View ArticleVariant annotations
Variant annotations are available to HaplotypeCaller, Mutect2, VariantAnnotator and GenotypeGVCFs. These are listed under Annotations in the Tool Documentation. HaplotypeCaller and Mutect2 calculate...
View ArticleHow to use multiple g.VCF files in GATK4.beta.1 GenotypeGVCFs?
Hi, I tried to use GenotypeGVCFs from GATK4.beta.1, but there seems to be still a bug with the --variants statement. At first I gave a list of my g.VCF files to it (ending .list as it worked in...
View ArticleJava error on running VariantRecalibrator
I have been trying tu run the VariantRecalibrator on my vcf with the standard command line suggested here:...
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