Difference between a 0/0 (hom.ref.) and ./. (no-call) genotype in...
I've called my samples with HapltypeCaller in GVCF mode, and then jointly called variants with GenotypeGVCFs. I've included a variant below. As you see, one sample is called homozygous reference 0/0,...
View ArticleQuestions about the RNAseq variant discovery workflow
This discussion was created from comments split from: Calling variants in RNAseq.
View ArticleFilterMutectCalls BUG
Dear GATK Team, I am writing you to discuss a an error while using FilterMutectCalls program and it seems a poential bug. I wanted to change the default value of **--normal-p-value-threshold **. It...
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MarkDuplicatesSpark java.io.IOException invalid null input: name
Hi everyone, I have recently tried to use MarkDuplicateSpark as part of my WES pipeline and replace the old picard's. I am using it on AWS from the docker image. I am new using Spark, so I cannot...
View ArticleHaplotypeCaller error: Badly formed genome unclippedLoc: Query interval is...
Hi there, I'm running the GATK best practice pipeline (locally on a Linux server without using docker) for Germline short variant discovery (SNPs + Indels) using the Generic germline short variant...
View ArticleDo I need to make PON for calling with mutect2(GATK3) in paired tissue sample ?
I guess it didn't have to make PON in paired (TN) tissue. but In BEST PRACTICE, it's good to make a PON although you have paired tissue for using mutect2. Thanks GATK team.
View ArticleAnalyzeCovariates exceptions
We are seeing this type of exceptions when running BQSR on our samples. Exception in thread "Thread-1" htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException:...
View ArticleGATK 3.8 with MTBseq
Hi, I am trying to use GATK with MTBseq and it states that you have to use v3.8 which cannot be installed by conda. I have installed using the following "conda install -c conda-forge -c bioconda gatk"...
View ArticleError in GermlineCNVCaller: Anomalous ploidy and karyotypes
I ran the GermlineCNVCaller on the GATK4 docker using data from Illumina WES runs: I saw one post about this from 2018, but there were no solutions provided. Was hoping someone figured out what might...
View ArticleDepth of coverage in GATK 4
Hello, I'm trying to find the depth of coverage for a targeted sequencing project using GATK 4, but I'm confused about which tool I can do this with. I've combed over the list of new tools and have...
View ArticleAberrant VQSLOD scores
Hello, I recently reanalyzed a large number (>10,000) of targeted exome sequencing bam files using GATK 4.1.0.0 following the gatk4-germline-snps-indels cromwell workflows (haplotypecaller-gvcf then...
View Article(How to) Run GATK in a Docker container
This document explains how to install and use Docker to run GATK on a local machine. For a primer on what Docker containers are for and related terminology, see this Dictionary entry. Contents Install...
View Article(How to) Install and use Conda for GATK4
Some tools in GATK4, like the gCNV pipeline and the new deep learning variant filtering tools, require extensive Python dependencies. To avoid having to worry about managing these dependencies, we...
View ArticleAD allele depth interpretation
Hello, I have a query on the interpretation of the AD variable in a vcf generated by calling about 800 samples together. The header defines it as: ##FORMAT= and the forum further elaborates: AD is the...
View ArticleA missing deletion in the tri-nucleotide repeat sequence using GATK-Mutect2...
Hi GATK team, I performed whole-exome seq, followed by variant calling by GATK-Mutec2 (v4.1.0.0). I found there is a deletion occurred in input Bam and bamout file in my two samples, however, the...
View ArticleMultisample SNP Calling
Hello! I'm trying to use GATK to call SNPs on multiple bam files (at once) but I encounter some "problems". I tried HaplotypeCaller and UnifiedGenotyper and it works well. The vcf is generated. But not...
View ArticleHow to use breakBandsAtMultiplesOf
I am using gatk3.7. combinegvcfs allows a large cohort to be called with genotypegvcfs. I also wish to use -L flag to combinegvcfs to shard the calculations by genomic location. Other guides also...
View ArticleCan one get bamout for the normal sample in Mutect2?
Is it possible to get a bamout for the normal sample in Mutect2? Is the local realignment performed also for the normal sample? I have several case samples where I get variants (exactly the same...
View ArticleSelectVariants - java.lang.IllegalStateException: Allele in genotype not in...
Hi everyone, I'm trying to select variants with SelectVariants but for some reason it stops saying that Allele in genotype CT* not in the variant context [CT*, C]. I tryied to find a CT* in the VCF...
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