different webadress for variant combining?
Hi, https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantutils_CombineVariants.php I need to get to the documentation for combining...
View ArticleRNAseq preferred reference - b37 or hg19?
Hi. I'm wondering if there's a preferred human reference build for aligning RNAseq data? The only factor that even leads me to ask this question is the following article...
View ArticleClik here to view.
Poor VQSR filtering
I ran VQSR on my vcf file from joint genotyping. I used dnSNP as training. The plots generated during VQSR don't seem to separate the pos and neg very well. Below are the plots for one sample. I use...
View ArticleMutect2 version 4.0.0.0
Mutect2 version 4.beta.6 ./gatk-launch Mutect2 --help BETA FEATURE - FOR EVALUATION ONLY Mutect2 version 4.0.0.0 ./gatk Mutect2 --help BETA FEATURE - WORK IN PROGRESS Is there a timeline for having a...
View ArticleWhat's in the resource bundle and how can I get it?
NOTE: we recently made some changes to the bundle on the FTP server; see the Resource Bundle page for details. In a nutshell: minor directory structure changes, and Hg38 bundle now mirrors the cloud...
View ArticleClik here to view.
MuTect2 Seems to lose a lot of mutations.
I use Mutect2 (tumor only mode) to find somatic mutation, but some position was not able find mutations. I have attached some IGV figures in the regions where MuTect2 has missed somatic mutations (Top...
View ArticleCromwell call-caching Failed to hash error
I get the following error when I enable call-caching in cromwell 30.1 2018-01-12 12:49:02,002 cromwell-system-akka.dispatchers.engine-dispatcher-57 ERROR - Failed to hash java.io.IOException: Is a...
View ArticleUpdated WGS pre-processing workflow
Dear GATK, -As per GATK 4.0.0 best practices guidelines, it is my understanding that no indel realignment step is performed anymore. Is this correct? If so, why not? -During the pre-processing stage of...
View ArticleGATK 4 missing tools
Please let me know what happened to Callable Loci; I do not see it in GATK 4's list of tools. Thank you for your assistance.
View ArticleValidateVariants Error on low coverage WGS variant calling
Dear GATK Team, first of all.. Thanks for the great work I love your software package. I am currently experiencing some problems on a low-coverage sequencing project. In a nutshell: We deep-sequenced...
View ArticleHaplotypeCaller error in the middle of processing
I run the GATK4 using this command: GATK4 HaplotypeCaller \ -I ${input_file}\ -R umd_3_1.fa \ -L ~/helper/location.bed \ -O ${file_name}.gatk4.g.vcf.gz \ -ERC GVCF \ And got error as follow:...
View ArticleMutect2 parallel problem
Dear GATK team. I am using Mutect2 to call somatic mutation from tumor/normal paired sample. However after jobs running for 8 days, our server has been rebooted for some reason. Most of the jobs are...
View ArticleClik here to view.
What are the differences between Mutect2 and HaplotypeCaller?
They share graph assembly and haplotype determination -- but the similarities end there Operationally, Mutect2 works similarly to HaplotypeCaller in that they share the active region-based processing,...
View ArticleVersion highlights for GATK version 4.0
The brand new 4.0 version of the GATK was released -- at long last! -- on Tuesday Jan 9, 2018. In lieu of our traditional version highlights, for this release we have collected the following resources:...
View Article(howto) Call variants with HaplotypeCaller
Objective Call variants on a single genome with the HaplotypeCaller, producing a raw (unfiltered) VCF. Caveat This is meant only for single-sample analysis. To analyze multiple samples, see the Best...
View ArticleNot double counting variants in overlapping SAM/BAM files using UMIDs and...
I am trying to move off home grown UMID tools I wrote to the new fgbio UMID toolset but I am trying to understand how I do this in a way that doesn't double count variation in the overlapping region....
View ArticleGATK 4.0.0.0 HaplotypeCaller Error with -L chrM
When running the GATK 4.0.0.0 HaplotypeCaller with the following: gatk HaplotypeCaller \ -R $REF \ -I $CRAM_DIR/$SAMPLE.cram \ --emit-ref-confidence GVCF \ -ploidy 1\ -L $TARGETS \ -O...
View ArticleUse all samples or group samples for GenotypeGVCFs?
I have created g.vcfs for all my samples (48). Half of my samples (24) are control individuals and the other half (24) is treated individuals. Should I run GenotypeGVCFs on all my samples once to...
View ArticleClik here to view.
Training a Filter on Truthset gathered by several Tumor-Normal analyses for...
Hi, I have the following project setup 150 matched tumor/normal samples and 100 tumor only samples from the same entity. I analyzed them all with Mutect2 using a PON which I build up from the normal...
View Article