I do not get the annotations I specified with -A
The problem You specified -A <some annotation> in a command line invoking one of the annotation-capable tools (HaplotypeCaller, MuTect2, UnifiedGenotyper and VariantAnnotator), but that...
View ArticleHow to create a coverage table for MutSig?
Hi, I am trying to use MutSig and would like to know if there is a way/script to generate coverage tables for the experiment under analysis. I have tried to use the standard exome_full192.coverage.txt...
View ArticleGenotypeGVCFs fails to complete in 10 days
I have been following the "HAPLOTYPECALLER GVCF - Exome/Panel + Whole Genome" best practices on a set of 13 whole-genome sequences from a non-model organism (~10x coverage). I have successfully created...
View ArticleCalling variants in non model organisms
Dear Gatk team, I've been going through your best practices workflow to clean up my DNAseq data. I have 4 whole genomes (20x depth) from two grape cultivars, two genomes from each cultivar, and we...
View ArticleIs it possible for GATK4 beta3 Mutect2 to output germline variants also?
By the default configuration, it seems that all variants are somatic. I could not find the parameter which would regulate that.
View ArticleHaplotype Caller Makes SNPs look like INDELS
I'm using the HaplotypeCaller to look at SNPs related to antimicrobial resistance and am getting a result that looks like this: NC_011035.1 2049708 . CCGGCG C ... NC_011035.1 2049714 . C CAAGAA ... I...
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Pre-processing for GATK pipeling: BWA necessary for SNPs discovery in genomic...
Hello, I am working with DNA capture, with paired-end sequences, that I plan to run into GATK pipeline for SNPs and InDel Discovery in genome data. On the website, GATK suggests to start the...
View ArticleDiscrepancy in GVCF file size between bam files of a similar size
Hi I am performing WGS analysis according to the GATK best practice guidelines (aligning to hg38). I am calling variants on my samples using HaplotypeCaller in GVCF mode to generate GVCF files (by...
View ArticleTesting different capture reaction template
I did a test of capture sequencing : 96 libraries representing 56 individuals For one individual we made 1,2,3 or 4 libraries. The libraries were pooled before capture reactions so that the same...
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 ArticleSame position, multiple alt alleles, no depth info - Why ?
Hello, Sorry for the simplistic question, but I am new at this. Using Mutect2 (and a few other callers) to look for somatic variants, we are getting multiple cases where several alt alleles are...
View ArticleWhat does MuTect output means?
Hello! Currently, I am working on identification of somatic mutations on exome data. For this, I am using the combination of GATK + MuTect2 using following code: java -jar...
View ArticleWhat do GATK workshops cover?
This is the description of our current 3-day workshop formula. 3-Day workshop summary This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit,...
View ArticlesvGenotyper Error: Null Pointer
SVpreprocess seemed to run without error for my samples. However I'm getting an error with svGenotyper ##### ERROR...
View ArticleError Running CNVDiscovery Pipeline
I tried to run the pipeline and it succeeded for the first stage but then failed at the second. It looks like a null pointer exception. What other information would be useful to debug this? INFO...
View ArticleHow to fix the error Unable to access jarfile GenomeAnalysisTK.jar
I have been trying to open the GATK and I always get the same error message: Unable to access jarfile GenomeAnalysisTK.jar. I have a Mac with OS X Yosemite. I also have the latest version of java...
View ArticleHi, i cannot open the program on MAC
Hi i run mac OS X el capitan. When i start the jar file i get an error message: The Java JAR file “GenomeAnalysisTK.jar” could not be launched.
View ArticleMixed PoN (Blood + FFPE) ?
Hi, I have some FFPE WGS data. I am able to access TCGA bam file. I want to build a PoN for mutation and CNA analysis with 900+ blood tissues (TCGA) and 30+ FFPE tissues (TCGA + my own). Does this PoN...
View ArticleVariantFiltration ArrayIndexOutOfBoundsException: 49
Hello, The VariantFiltration tool output an ArrayIndexOutOfBoundsException: 49 error when processing a VCF produced by gatk tools HC/GenotypeGVCFs followed by SelectVariants to split out SNPs. I...
View ArticleSubset CombinedGVCF files?
Hello, We're in the middle a project where we are iteratively generating variant data on what is a large and growing cohort. We we're adding data to the existing cohort in batches of ~96. For each...
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