GATK4-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 ArticleGenotype "./." with depth 150 - GenotypeGVCFs
Hello GATK Team, I have a question regarding GATK "GenotypeGVCFs". I found some variants showed genotype "./." with resonable read depth from result file from "GenotypeGVCFs". Genotype of...
View ArticleRead groups
There is no formal definition of what is a read group, but in practice, this term refers to a set of reads that were generated from a single run of a sequencing instrument. In the simple case where a...
View ArticlePicard SortVcf fail for no reason ?
Hello, Command line(s) you ran: java -jar picard.jar SortVcf I=cosmic/cosmic.vcf O=cosmic/cosmic.srt.vcf SD=reference/GRCh38.d1.vd1.dict Program console output and metrics files. Repetitive console...
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Mutect2 with GATKv4
Hi, I'm trying to run Mutect2 with GATK4-alpha. The program seems to start, then just stalls and doesn't produce any output. My command is: java -jar ../gatk-protected-local.jar Mutect2 -R...
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Variant calling inconsistencies using GVCF
Before starting, I'm a grad student without formal training in bioinformatics so I've mainly learned from online forums. That being said, if this question is stupid or I'm missing critical information,...
View ArticleHelp recalling a set of bams
Hi Broad folks, I am looking for a little bit of guidance recalling some bams (which were actually sequenced at the Broad as well). I have been working through the workflow described here, which has...
View ArticleError with RealignerTargetCreator
I run GATK RealignerTargetCreator last week and it worked. But today when I run it, it shows this error. I have no idea what happened. Anyone can help? Appreciate ahead. ERROR MESSAGE: Invalid command...
View ArticleGATK v4 Variant Recalibrator command line
Could someone please provide me with a sample command line to run Variant Recalibrator for GATK v4? I am running the tool using GATK 4 Alpha with the following command line:...
View ArticleUsing JEXL to apply hard filters or select variants based on annotation values
1. JEXL in a nutshell JEXL stands for Java EXpression Language. It's not a part of the GATK as such; it's a software library that can be used by Java-based programs like the GATK. It can be used for...
View ArticleIs it safe to call variants per chromosome when using HaplotypeCaller?
Hi! I'm calling variants in a cohort of samples following the best practices recommendations...
View ArticleVariant Filtration isn't working
I'm trying to filter a vcf file with SNPs using the following code: java -jar GenomeAnalysisTK.jar \ -T VariantFiltration \ -R reference.fasta \ -V My_Snps.vcf \ --filterExpression "DP < 10 || DP...
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Calling variants on cohorts of samples using the HaplotypeCaller in GVCF mode
This document describes the new approach to joint variant discovery that is available in GATK versions 3.0 and above. For a more detailed discussion of why it's better to perform joint discovery, see...
View ArticleWhen should I use -L to pass in a list of intervals?
The -L argument (short for --intervals) enables you to restrict your analysis to specific intervals instead of running over the whole genome. Using this argument can have important consequences for...
View ArticleNo plots generated by AnalyzeCovariates in GATK4-Alpha
I'm using GATK4-Alpha AnalyzeCovariates java -Xmx80G -jar $GATK AnalyzeCovariates -before recal.table -after after_recal.table -plots recal_plots.pdf The tool appears to finish however I then get an...
View ArticleI am unable to use VQSR (recalibration) to filter variants
The problem: Our preferred method for filtering variants after the calling step is to use VQSR, a.k.a. recalibration. However, it requires well-curated training/truth resources, which are typically not...
View ArticleProblemm with hard filtering
Hi All, I am trying to use GATK for variant filtration (hard filtering) for non human species, using the below command after choosing SNPs only: java -d64 -Xmx48g -jar...
View ArticleWhat are the standard resources for non-human genomes?
We're trying to put together some recommendations for folks who want to use GATK tools on non-human genomes. But we really don't have much experience with non-human genomes, so we're hoping that those...
View ArticleBCL to uBAM tutorial update
Hi there, I'm very interested on try the BCL to uBAM protocol (Tutorial#6570 coming soon) you have mentioned on your article #6483 ((How to) Map and clean up short read sequence data efficiently). Do...
View ArticleGermline mutation with t_alt_count 0 identified with GATK
I used GATK tools haplotypecaller and GenotypeGVCFs, and identified germline mutations. One of the mutations look like after GATK GenotypeGVCFs" V1 V2 V3 V4 V5 V6 V7 1 16257 . G C 44.77 . V8...
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