SelectVariants
Hi, I'm using SelectVariants to process VCF file downloaded from ftp-mouse.sanger.ac.uk/current_snps/. This vcf contains SNPs for many mouse strains, and I need to extract information for only two...
View Article(howto) Test your GATK installation
Objective Test that the GATK is correctly installed, and that the supporting tools like Java are in your path. Prerequisites Basic familiarity with the command-line environment Understand what is a...
View Article(howto) Recalibrate base quality scores = run BQSR
Objective Recalibrate base quality scores in order to correct sequencing errors and other experimental artifacts. Prerequisites TBD Steps Analyze patterns of covariation in the sequence dataset Do a...
View ArticleAWS Service is down, what's an alternative to run GATk VariantsToTable?
Hi I'm running the following command: java -Xmx56g -Djava.io.tmpdir=$workDir/tmp -jar /share/apps/gatk/3.4-46/GenomeAnalysisTK.jar -T VariantsToTable -R $refGenome --allowMissingData...
View ArticleAnalyze covariate plots
Hi, I have used AnalyzeCovariates to plot the before and after recalibration results. I noticed that the quality scores in insertion and deletion panel are quite high, is this normal? For covariates...
View ArticleIs it possible to suppress the NON_REF tag on variant calls?
Hello, In GVCF output from HaplotypeCaller, each line contains the allele, including the lines with explicit variant calls. Is there a simple way to suppress the allele on variant calls? Also, what is...
View ArticleMuTect2: ERROR MESSAGE: Somehow the requested coordinate is not covered by...
Hi guys, I use mutct2 to do somatic variant calls, and got this ERROR MESSAGE: Somehow the requested coordinate is not covered by the read. Too many deletions? I searched the forum and found people got...
View ArticleAnnotation for the genome in the boundle
Hi, I did a RNA-seq GATK analysis with a genome supplied in the bundle - human_g1k_v37_decoy.fasta. I would like to find corresponding annotation to this genome, which is not supplied in the bundle....
View ArticleError running the GATK WDL best practices pipeline
Hello, I am running the GATK WDL best practices pipeline with the sample data from the Google Cloud...
View ArticleHaplotypeCaller exits silently
Dear GATK team, I recently upgraded from GATK 3.3 to GATK 3.7 and I started encountering some problem with HaplotypeCaller apparently related to the allocated memory. I started to run it with 24GB...
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 ArticleCalling all variants in amplicon library with read counts
Hi! I am trying to determine the composition of a single gene library. My amplicon is 750 bp long and was sequenced with Illumina 2x75 bp paired-end kit. Because the amplicon library was constructed to...
View ArticleMutect2 --artifact_detection_mode for tumor-only calling : can i use PoN
I am aware that "Tumor-only variant calling is possible but it is not supported with Mutect2". Thing is, i am working on a study with few normals. I did create my PoN with the 10 available normals. I...
View Articlecan ValidateSamFile check on CRAM files?
I'm trying to validate a set of cram files, however, I'm getting the error shown below. I'm not sure if it is because I'm using a CRAM file, I have problems with the htsjdk library or the cram files...
View ArticleWhich training sets / arguments should I use for running VQSR?
This document describes the resource datasets and arguments that we recommend for use in the two steps of VQSR (i.e. the successive application of VariantRecalibrator and ApplyRecalibration), based on...
View ArticlePicard slow I/O on a parallel filesystem
Dear support, I have been trying to make picard bamtofastq run faster by using all tricks in the book, but it seems to bound itself to some 1.2 MB/s no matter what I do. Is the problem creating locks...
View ArticleZero Depth with Genotype?
Hello, I'm using GATK and I found this - "zero depth with genotype" As INFO column said, DP=54, however, in sample column DP:0 with GT:1/1. And reads are found by looking bam file with samtools tview....
View ArticleGenotype 1/1 with total depth 0 in VCF file from Haplotype Caller
Hi. I am looking at a VCF file with SNV results from Haplotype Caller, using GATK version 3.5. I've noticed one call reporting the following description 1/1:0,0:0:3:1|1:17764184_CG_C:6,3,0 (format...
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What is a VCF and how should I interpret it?
This document describes "regular" VCF files produced for GERMLINE calls. For information on the special kind of VCF called gVCF, produced by HaplotypeCaller in -ERC GVCF mode, please see this companion...
View ArticleWhy Are Students Using Online Essay Writing Services ?
In recent years, online freelancing jobs have skyrocketed. It has come to a point where these sites are reviewed and rated based on different factors to provide users information on which essay writing...
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