about JEXL and replacing in SelectVariants()
Dear all, good afternoon. I would appreciate please an insight on the following : I am using SelectVariants to select the HETEROZYG and it is working : $GATK \ -T SelectVariants \ -R...
View Articleabout ASEReadCounter
Dear all, i am using ASEReadCounter in order to count the number of reads per variant in a BAM file, and somehow related to a previous post (below), I am encountering a similar error : "MESSAGE: More...
View ArticleERROR: Badly formed genome location... when I run Joint genotyping with a...
I have processed exome seq files following GATK Best Practices. I was to run joint genotyping with a interval list (format: BED) and faced with an error message like this: ERROR MESSAGE: Badly formed...
View ArticleMuTect2: complex variant expression
Hi, I use GATK3.7 MuTect2 to call somatic variant: here is the command: java -jar GenomeAnalysisTK.jar -T MuTect2 -R hg19.fasta -I:tumor tumor.bam -I:normal normal.bam --dbsnp dbsnp_138.hg19.vcf...
View ArticleHaplotype caller (GATK 3.7) warning message for InbreedingCoeff
Hi, I am running HC with both .g.vcf and bamout as parameters. The command executes successfully, but with warning message: Annotation will not be calculated. InbreedingCoeff requires at least 10...
View ArticleERROR: GATK VQSR fails to identify top worst variants and terminates
Hi, I've been using GATK's VQSR to my satisfaction in multiple projects, however, today have encountered the same failure on multiple seemingly normal exomes. Here's the log. INFO 16:01:37,398...
View ArticleWhere can I find the GDC mutect2 version?
Hello, The GDC docs here indicate a particular GATK nightly build "GATK nightly-2016-02-25-gf39d340", which is not available in the GATK nightlies download site here. So my question is, can I still...
View Articlemissing mutation in TP53
Dear all, we have been doing a WES analysis, and we have used MUTECT2 to call the mutations in a situation where we had : 1) -- a tumor sample 3) - unpaired 3 germline samples (that 've pooled...
View Articlefiltering a trio joint VCF based on GT DP
Hi I have a joint VCF with a trio of samples in it, and would like to only retain those sites where all 3 samples have at least DP >=10 in their respective GT FORMAT field. I have been trying to do...
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ERROR MESSAGE: Code exception
I got this error during local realignment ERROR ------------------------------------------------------------------------------------------ ERROR stack trace java.lang.InternalError at...
View Article[WDL][Cromwell[ Mounting a directory to the docker for access.
Hi, I am attempting to run Gemini within a docker through WDL and Cromwell. I have installed gemini with no data as the data is too large to be put into a Docker (plus it's bad practice). So I need to...
View ArticleEvaluating the quality of a variant callset
Introduction Running through the steps involved in variant discovery (calling variants, joint genotyping and applying filters) produces a variant callset in the form of a VCF file. So what’s next?...
View ArticleREGARDING COMBINING VARIANTS IN CLOUDMAP IN GALAXY
Hi I am new to sequencing and i tried with galaxy i am done with vcf files of all mutants and now i have to combine variants but its showing error the tool is as follows...
View ArticleHow can I increase the sensitivity of my initial GATK exome variant calling?
I am following the best practices for GATK exome variant calling, but am failing to cast a wide net and catch all validated SNPs on my first pass variant calling. As a test, I have download the NA12878...
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MuTect2 : Calling on triallelic_site by GATK v3.6 vs v3.7
Here is different calling result on specific tri-allelic site using GATK v3.6 and v3.7. [ Command ] java -XX:ParallelGCThreads=6 -Xmx30g -jar GenomeAnalysisTK-3.6 (3.7) /GenomeAnalysisTK.jar...
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 Articlerules for max_alternate_alleles in HaplotypeCaller
Hi, I can't come to any clear conclusion how this parameter works. Help me, please. I worked on the same files with exact command but the max_alternate_alleles. In first command I put 1 for its...
View ArticleEffect of running BQSR per sample and not lane
What is the effect of running BQSR per sample across lanes and not per sample per lane i.e if @RG ID is per sample and not per sample lane. Does it introduce additional errors or just run BQSR...
View ArticleASEReadCounter: Lexicographically sorted human genome sequence detected in...
I have aligned RNA-seq files using STAR with reference file Homo_sapiens.GRCh37.dna.primary_assembly.fa. I have created a dict file for the fasta file using CreateSequenceDictionary. I have ordered my...
View ArticleMuTect2 and VQSR: anyway of calling VQSLOD for MuTect2 ?
Hello GATK Team ! @Sheila @Geraldine_VdAuwera Since my last question ( here ), I am trying to build a workflow which can process all my samples with a snakemake workflow. From the previous question...
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