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Can I use GATK on non-diploid organisms?
In general most GATK tools don't care about ploidy. The major exception is, of course, at the variant calling step: the variant callers need to know what ploidy is assumed for a given sample in order...
View ArticleCannot get HaplotypeCaller to output phase information in pooled multi-sample...
There is currently no way to run HaplotypeCaller with pooled multi-sample calling and still get phasing output. By pooled multi-sample calling, I'm referring to running HaplotypeCaller to...
View ArticleWhy is HaplotypeCaller not calling this Sanger sequencing confirmed variant?
Hi, I am using HaplotypeCaller in GVF mode and GenotypeGVCFs to call some high-depth targeted sequencing data. I have some variants that have been confirmed using Sanger sequencing and I am using these...
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 ArticleIlluminaData is missing error in Picard IlluminaBasecallsToFastq
I am using Picard 2.7.1 with Java 1.8 to demultiplex Illumina sequencing data from BCL to FASTQ. I am using the commands: java -Xmx2000m -jar ExtractIlluminaBarcodes LANE=1 OUTPUT_DIR=path_to_output...
View ArticleGATK 3.6 always re-creates a tribble index for input VCF file instead of just...
Hi, like other I get some of my cluster jobs crashing with: ERROR -- ERROR stack trace java.lang.RuntimeException: java.lang.reflect.InvocationTargetException at...
View ArticleTranches plot issue
Hi Geraldine, I think that this question has been asked before but I cannot find the way to fix the problem. I have just run VariantRecalibrator tool, and I'm getting this (see attached file) tranches...
View Article(howto) Install and run Oncotator for the first time
1. Download the Oncotator package, the default datasources package, and (recommended) transcript override list from the Downloads page Please note: Broadies who wish to run the installed Oncotator on...
View ArticleRun GenotypeGVCFs by populations separately or all populations together ?
Hi GATK team, I have a question about joint genotyping which I think has not been addressed yet in this forum. I want to do population genomics on a non model species. Once I have my gVCFs files for...
View Articleg.vcf masks variants with conflicted reads
I'm working on Salmonella, and one of the major sources of noise in our analysis is that there are some regions of the genome where we have many reads that disagree with the eventual call at that...
View ArticleRunning HaplotypeCaller in GENOTYPE_GIVEN_ALLELES mode with...
Hi Sheila and Geraldine When I run HaplotypeCaller (v3.3-0-g37228af) in GENOTYPE_GIVEN_ALLELES mode with --emitRefConfidence GVCF I get the error: Invalid command line: Argument ERC/gt_mode has a bad...
View ArticleBUG: java.lang.IllegalStateException: The original PLs do not have enough values
I have run HaplotypeCaller (Version=3.1-1-g07a4bf8) on 99 WGS samples and created my GVCFs. I did this in 60+ intervals to enable faster turn around time. I then merged the GVCFs with CombineGVCFs...
View Articlemany `LowQual` flags in output .vcf when using `HaplotypeCaller` with...
Hi GATK team, I am working on a pipeline for exome sequencing variant calling. And I am only interested in the genotype for some specific positions so I used GENOTYPE_GIVEN_ALLELES mode with given vcf...
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Calling variants on cohorts of samples using the HaplotypeCaller in GVCF mode
This document describes the new approach to joint variant discovery that is available in GATK versions 3.0 and above. For a more detailed discussion of why it's better to perform joint discovery, see...
View ArticleWhats the Reseaon for using GATK4-BQSR in your PublicPairedSingleSampleWf
Hi Folks, is there any benefit from using the GATK4-Version of BQSR ? Harder, Better, Faster, Stronger ?;) Greetings, EADG
View ArticleRationale behind MuTect2 and Haplotype Caller
Dear GATK team, I would like to better understand MuTect2 and HaplotypeCaller in order to present the methods, as I am doing a Thesis on Somatic Mutation Discovery. Unfortunately the only reference...
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(How to) Map reads to a reference with alternate contigs like GRCh38
Document is in BETA. It may be incomplete and/or inaccurate. Post suggestions to the Comments section. This exploratory tutorial provides instructions and example data to map short reads to a reference...
View ArticleisCalled, isNoCall, and isAvailable in Genotype Filtering
Greetings, The VariantFiltration documentation mentions the availability of isCalled, isNoCall, and isAvailable methods in genotypeFilterExpression. I find it quite misleading because filters are...
View ArticleBAMs with multiple RG lines
Hi, I have a set of BAMs, of them most contains multiple RG lines (same sample were run multiple times sequencing). Now I need to run GATK HC caller (the BAM-> g.vcf -> vcf route), it complains...
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