StatusLogger Log4j2 could not find a logging implementation.
I have been trying to use RealignerTargetCreator for treating my INDELS. My command is : nohup java -jar /data/ngs/programs/GenomeAnalysisTK-3.8-0-ge9d806836/nightly/GenomeAnalysisTK.jar -T...
View ArticleClik here to view.
Parallelism
This document explains the concepts involved and how they are applied within the GATK (and Crom+WDL or Queue where applicable). For specific configuration recommendations, see the companion document on...
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 ArticleSNP Calling issue- Haptotype caller not calling all SNPs
Hi I am working with Candida albicans genome for SNP calling. Its Whole genome data. I used standard steps used here https://gencore.bio.nyu.edu/variant-calling-pipeline/ I am finding a very strange...
View ArticleWhat is truth? Or, how an accident of nature can illuminate our path
A note to explain the context of the new paper by Heng Li, myself and others, “New synthetic-diploid benchmark for accurate variant calling evaluation” available as a preprint in bioRxiv. Developing...
View ArticleGenomicsDBimport multijob issue
I'm having a strange problem with GenomicsDBImport. I'm trying to call SNPs for the full genome, so I've been importing my g.vcfs into a GenomicsDB database per chromosome. Each chromosome is a...
View ArticleCreatePanelOfNormals problem
I am trying to ues CreatePanelOfNormals for cnv analysis java -Xmx4G -jar /ifshk7/BC_PS/luoshizhi/software/gatk/gatk-4.beta.2-4/build/libs/gatk.jar CreatePanelOfNormals -I...
View ArticleWhat is a good number of samples that can be used to detect a variant - I...
Hi, I have 15k GVCFs. To call variants, I understand I can run combineGVCFs step to get batches of GVCF combined. I would like to know whats the good number for a sample set, for bams with coverage of...
View ArticleClik here to view.
(How to) Call somatic copy number variants using GATK4 CNV
This demonstrative tutorial provides instructions and example data to detect somatic copy number variation (CNV) using a panel of normals (PoN). The workflow is optimized for Illumina short-read whole...
View ArticleRealignerTargetCreator hangs with the nightly version...
I was having a "ERROR StatusLogger Log4j2 could not find a logging implementation" error and I tried to rectify it with the nighly build but with no avail The version of nightly build is :...
View ArticleUndefinend variable on Variantfiltration
Dear all!! I have tried to use the VariantFiltration (hatk 3.8) but the programs seem not gave me the results I expected. This is an example part of my vcf. You can see the variable AD are prest: es. 8...
View ArticleRealigner Target creator shows runtime error
I've been trying for over three months now and realigner target creator consistently shows runtime error. Is there a fixfor this? If not, is there an alternative that i can use?
View ArticleClik here to view.
Reference Genome Components
Document is in BETA. It may be incomplete and/or inaccurate. Post suggestions to the Comments section. This document defines several components of a reference genome. We use the human GRCh38/hg38...
View ArticleQuestion and suggestion re -nct & -num_threads options
Hi, I'm trying to implement a workflow with GATK for the first time and I'm getting caught out by the -nct/-num_threads options not being compatible with all walkers, erroring and then killing the...
View ArticleShould CheckIlluminaDirectory be able to handle a non-standard read structure
I have a flowcell (from a 10x library) in which the 'natural' read structure is 178T8B14B5T. However, I want to interpret the flowcell as 178T8B14T5S, so that is what I passed to...
View ArticleRealignerTargetCreator hangs
Hi GATK team! we have an issue with running the RealignerTargetCreator unfortunately. Commandline looks like this: gatk -T RealignerTargetCreator -R ref.fasta -I /testsample.sorted.bam -nt 32 -o...
View Articlewhy aren't my variants phased with PBT ?
I am running phasebytransmission on a trio vcf file. I am getting Zero phased genotypes, I couldnt figure out why: This is the output of thr run: ERROR StatusLogger Unable to create class...
View Articlecatch22 for filtering reads using FilterSamReads
Hi, trying to prepare some BAM files using picard/MarkDuplicates I got a SAM validation error (Padding operator not between real operators in CIGAR) for a few reads. I figured I'd remove them using...
View ArticleCRAM support in GATK 3.7 is broken
I have not been able to get GATK 3.7 HaplotypeCaller to work with CRAM files at all (it has a 100% failure rate so far with our whole genome CRAMs). Based on my analysis of the problem, I don't think...
View Articlejava.lang.ArrayIndexOutOfBoundsException in BaseRecalibrator on Grc38
I get a consistent failure with BaseRecalibrator on a handful of samples. It occurs with every version of GATK from 3.5 to 3.8 and the current nightly build. I've also tried altering the max memory...
View Article