VariantFiltration not filtering correctly
Hi, I'm running the following command to hard-filtering some variants: gatk -R /Users/debortoli/Doutorado/hg19/hg19.fa \ -T VariantFiltration -V vcf_no_indels.recode.vcf \ --filterExpression...
View Article(howto) Run the genotype refinement workflow
Overview This tutorial describes step-by-step instruction for applying the Genotype Refinement workflow (described in this method article) to your data. Step 1: Derive posterior probabilities of...
View ArticleErrors about read group (RG) information
What are read groups? See the Dictionary entry on read groups. Errors about missing or undefined read groups As detailed in the FAQs about input requirements, GATK expects all read groups appearing in...
View Articleusing multiple threads while running GATK4 on local server
Dear GATK Team, As GATK-4.0.0.0 released, and there are many new tools are also incorporated in this release. I wonder how to utilize the multiple thread options for GATK-4.0 and which tools are...
View ArticleSpam issue on the forum
We're aware that there is an unusually large amount of spam flooding the forum right now and are working with our host to address this issue. We may need to restrict access on a temporary basis. Our...
View Article(How to) Filter on genotype using VariantFiltration
Before using VariantFiltration, please read the entirety of the discussion in https://github.com/broadinstitute/gatk/issues/5362 that describes VariantFiltration's unintuitive behavior when processing...
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About haplotypecaller (one bam to one vcf)
Dear GATK team. Hi, I have a question. I have seen this presentation. I obtatined this presentation file from GATK google cloud. At the top of this figure, it is described as single sample BAM -->...
View ArticleVersion highlights for GATK version 3.8
One more 3.x version, for the road! That's right, even as we're ramping up our efforts on GATK4 (we're three beta releases in at this point, and getting down to brass tacks writing the migration guide...
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Differences between GATK3 MuTect2 and GATK4 Mutect2
Tool names are cased differently The first thing to note is how the tool names are different. In GATK3 it's spelled MuTect2 with an uppercase T, whereas in GATK it's spelled Mutect2 with a lowercase t....
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Somatic calling is NOT simply a difference between two callsets
To better understand what somatic calling entails, we contrast it to germline calling. We delve into the technical details of what is the same and what is different between Mutect2 and HaplotypeCaller,...
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Goodbye GATK Forum
Dear GATK users, I am writing this blog post to let you know it has been a wonderful 4+ years working on the forum and answering your questions. Thank you all for giving me a job for all this time and...
View ArticleGQ=0 but GT=0/0
GATK calls for SNP rs429358 don't look quite right in our project level vcf. This is one of the two SNPs that define the APOE e2,e3 and e4 (so just 3 haplotypes in region). About 1% of the 5000 samples...
View ArticleGenotypeGVCFs hanging?
I'm trying to call genotypes on ~160 S. cerevisiae genomes by going calling. When I tried to do it on the whole genome with a single command, it would run out of memory (even with 48G provided). Now...
View ArticleExtracting de novo mutation from multi sample vcf
Hi all, I'm currently trying to extract de novo mutations from my multi-sample vcf files (trios). I've already read the VCF file specification documentation but wanted to check if I got this right. So...
View Articleis mutect2 still in beta and can not be used for production , which function...
CreateSomaticPanelOfNormals is talked in https://software.broadinstitute.org/gatk/documentation/article?id=11136. while CombineVariants in...
View ArticleReference for GATK gCNV?
I'd like to reference gCNV in a paper I am writing. Is there a preferred way to do this?
View ArticleInfuence of Coverage Depth Difference in Tumor & Normal Sequencing Data in...
Hi, GATK team. I'm planing to use Mutect & Mutect2 to call somatic mutations in Tumor and mathched Normal samples. I have a question about the coverage depth difference of Tumor and Normal samples....
View ArticleRNA-seq SNP and INDELS
This discussion was created from comments split from: New to the forum? Ask your questions here!.
View ArticleERROR MESSAGE: Bad input:We encountered a non-standard non-IUPAC base in the...
Hi, I'm currently working with bwa, samtools and GATK to make SNP calling on Medicago truncatula. I'm using my own reference sequence, with the 8 chromosoms in the same fasta file. C1_lenght=155648...
View ArticleAll sites labeled as PASS after applying VariantFiltration to GenotypeGVCFs...
Hello! I run VariantFiltration on my joint-called SNP and indel set vcf file (HaplotypeCaller -> CombineGVCFs -> GenotypeGVCFs). I applied the following command in GATK4.0.6.0: gatk...
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