VariantRecalibrator: ERROR MESSAGE: NaN LOD value assigned.
I have some gVCF files, and I need to call variants from them. I am able to use HaplotypeCaller successfully, but VariantRecalibrator is giving me error. java -jar /storage/s1saini/GenomeAnalysisTK.jar...
View ArticlePicard vcf filtering
Hi, I use Picard to filter a vcf file. It seems not to function propely. I am filtering on read depth using MIN_DP=50 but I still see a lot of genotypes in the resulting file with lower coverage than...
View ArticleRun GATK on files stored in AWS S3?
Hi, Same as title: Is it possible to run GATK on files stored on S3?
View ArticleVCF input and BaseRecalibrator error
I'm trying to run BaseRecalibrator with GATK4-Alpha. I'm using --knownSites to input a vcf file as follows: java -Xmx80G -jar $GATK BaseRecalibrator \ -R reference.fa \ -I ${SAMPLE}_dedup.bam \...
View ArticleVariant detection in RNAseq: when to merge samples
Hi, I have followed the recommendations for my RNAseq variant search as outlined here: http://gatkforums.broadinstitute.org/gatk/discussion/4067/best-practices-for-variant-discovery-in-rnaseq Since I...
View ArticleMutect is not working
Dear Cancer team, I installed mvn, gatk-protected, and mutect. (https://github.com/broadinstitute/mutect) After that, I came upon the following error message: ERROR...
View ArticleVQSLOD score different for Full and split (by chromosome) BAM file
Dear all, I am trying to generate VCF using full and split (by chromosome) BAM files by GATK but after successful completion, there are difference in the VQSLOD score: For full : VQSLOD=-6.339e-01 For...
View ArticleClik here to view.
Genotype Refinement workflow
Overview This document describes the purpose and general principles of the Genotype Refinement workflow. For the mathematical details of the methods involved, please see the Genotype Refinement math...
View ArticleEmpty ContEst Output
Hello, I have some truseq cancer panel amplicon data and I am in process of calling Somatic variants in Tumor samples with MuTect. By using the default fraction_contamination, I am not getting any...
View Articlevariant calling with biological replicates
I am new to use GATK pipeline for SNP calling. I am currently working on four different populations (RNASEq data) with 6 clones. Each clone has 3 biological replicates. How do I combine the variant...
View ArticleI get very different MQ values when using GVCF vs BP_RESOLUTION
Hello! I had a question about the difference between using HaplotypeCaller's --emitRefConfidence GVCF vs BP_RESOLUTION. Maybe the answer is obvious or in the forum somewhere already but I couldn't spot...
View ArticleWeb-based Oncotator server
There is a web-based version of Oncotator which you can use for annotation without running anything on your own machine. However, please note that the web-based version is an older version, with fewer...
View ArticleAdvice for running GenotypeVCF and Recalibration on a thousand samples
Hi, I am working with a couple thousand gVCFs. I plan to run GenotypeGVCF and ApplyRecalibration on them in a joint fashion. I want to know how does GATK scale on these numbers, and is it even...
View ArticlePosters on somatic analysis with GATK4 presented at AACR 2017
A few of us GATKers (among a flood of other Broadies) traveled to Washington, DC this week for the General Meeting of the American Association for Cancer Research (AACR). Here are PDF copies of the...
View ArticleAnticipate "--fix_misencoded_quality_scores"
Hello everyone, I've created a full Variant Calling pipeline (on Galaxy). There is of course the IndelRealignment phase done by GATK. We all know now the solution of the "SAM/BAM file x appears to be...
View ArticleQuestions about DepthOfCoverage
This discussion was created from comments split from: Using DepthOfCoverage to find out how much sequence data you have.
View ArticleClik here to view.
Best Practices for Variant Discovery in RNAseq
This article is part of the Best Practices documentation. See http://www.broadinstitute.org/gatk/guide/best-practices for the full documentation set. This is our recommended workflow for calling...
View ArticleHow can I access the GSA public FTP server?
NOTE: This article will be deprecated in the near future as this information will be consolidated elsewhere. We make various files available for public download from the GSA FTP server, such as the...
View ArticleHow can I invoke read filters and their arguments?
Most GATK tools apply several read filters by default. You can look up exactly what are the defaults for each tool in their respective Technical Documentation pages. But sometimes you want to specify...
View ArticlePurpose and operation of Read-backed Phasing
This document describes the underlying concepts of physical phasing as applied in the ReadBackedPhasing tool. For a complete, detailed argument reference, refer to the tool documentation page. Note...
View Article