GermlineCNVCaller: transition matrix priors
Hi, I'm giving the Beta GermlineCNVCaller a spin and downloaded the CN_transition_matrix files from the GATK bundle at...
View ArticleGATK4beta6 annotation incompatibility between HaplotypeCaller and...
Happy New Year! I'm attempting to joint genotype ~1000 exomes using GATK4. I've run HC per sample with the following command: java -Xmx7g -jar gatk-package-4.beta.6-local.jar HaplotypeCaller -ERC GVCF...
View ArticleGATK4beta6 HaplotypeCaller doesn't index g.vcf.gz output
With the following command: java -Xmx7g -jar gatk-package-4.beta.6-local.jar HaplotypeCaller -ERC GVCF -G StandardAnnotation -G AS_StandardAnnotation --maxReadsPerAlignmentStart 0 -GQB 5 -GQB 10 -GQB...
View ArticledbSNP_RS seems to not be annotated with Oncotator 1.9.3
Oncotator 1.9 seems to not be annotating dbSNP annotations (dbSNP_RS), leaving all elements blank in this column. Other annotations are correctly annotated. My command line is oncotator -v --db-dir...
View ArticleWhen should I use -L to pass in a list of intervals?
The -L argument (short for --intervals) enables you to restrict your analysis to specific intervals instead of running over the whole genome. Using this argument can have important consequences for...
View ArticleGATK 3.8 No data Found
Hi,I ran VariantRecalibrator to do the VQSR,first I got the ERROR message 'Unable to retrive the result' and I remove nt parameter. Then I got the following error message. I also saw Geraldine_VdAuwera...
View ArticleAllele-specific annotation and filtering
Introduction and FAQs The current recalibration paradigm evaluates each position, and passes or filters all alleles at that position, regardless of how many alternate alleles occur there. This has...
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Running preprocessing steps on WGS and WES
Hello, I would like to run GATK on my sequence. The input to the process is FASTQ files and the output should be a clean BAM ready for variant calling. Could you please let me know what pipelines are...
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WES : too many variants ?
Hi! I'm working on exome sequences. My colleague used the following pipeline (GATK 3.7) : 1) bwa mem (reference genome : GRChr37) => sam 2) samtools view -bS -F 0x04 **(eliminates unmapped reads)...
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What are the smallest units I can break whole human genomes into, for...
Hi, and thank you so much for the wonderful tools and support! For our current project, we'd like to run 2000+ whole genomes from FASTQ to VCF using GATK best practices. I'd like to optimize the...
View ArticleGenotype DP information missing in multisample vcf
I used genotype gvcfs from 10 gvcf's - emitting all sites to get an all sites vcf (i'm interested in both variant and invariant sites). I get some sites where there is DP in the INFO column, but DP...
View ArticleCollectRnaSeqMetrics - RIBOSOMAL_BASES
Hi, I am having a problem with RIBOSOMAL_BASES estimated as 0. When I open the mapped reads I observe several reads at ribosomal positions. The same problem is discussed in another forum but no...
View ArticleProtocol for ploidy data
Hi I have 3 allo-tetraploid genome( like cotton) fro snps analysis while calling snps ploidy will be set to 2 or 4?
View Articlehow to order scaffolds and organize into putative chromosomes with BWA-MEM
Hello everyone, I want to do Fst analysis about two populations, but I just have vcf file, so i want to know how to order scaffolds into chromosomes with BWA-MEM tools that I can do the Fst analysis....
View ArticleGenotypeGVCFs: Long runtime exclusively with a single sample
I have been having some trouble with long runtime with several of GATK utilities. However it was manageable. I could arrive at a g.vcf file( I used HaplotypeCaller instead of UnifiedGenotyper upon a...
View ArticlePolysolver: input BAM question
Is there any advantage in launching the pipeline with a whole-genome bam? I was thinking that pulling out from the original BAM unmapped reads plus reads mapped to the HLA-locus could be ok and make...
View ArticleInput files known and reference have incompatible contigs
I have a question. I use the GATK RealignerTargetCreator, I have this error message. ERROR MESSAGE: Input files known and reference have incompatible contigs: Found contigs with the same name but...
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PGT and PID is a dot
Hi, I am following the best practice pipeline with version 3.6 of gatk and in order to reduce the amount of compound heteozygote variants found in my analysis, I recently chose to "mature" into using...
View ArticleCatVariant does not work.
Hi there, do you know why I got this error when I try to use CatVariant ? java -Xmx10G -jar /Users/xxx/bin/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.CatVariants \ -V...
View ArticleHeads up: documentation and website updates for GATK4
With less than a week to go before the big day (aaaaaaah), we're putting the finishing touches on some important updates to the website and the documentation. Starting Tuesday Jan 9, the primary...
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