[INSTALLTEST] Discovery.sh --> VCF is missing
Hi everyone I tried to launch the install test script (discovery.sh). All seems to work : no error in the logs, no error in the stderr. But at the end, I have this message : INFO 10:29:26,082...
View ArticleSplitNCigarReads unrecognized options
Hi, I've been following the "Calling Variants in RNASeq" workflow, using the most recent version of gatk (v4.0.2.1). When I run the SplitNCigarReads command I get the following error: $gatk...
View ArticleHow do you know when SVPreprocess has successfully finshed?
I apologize in advance if this is a stupid question. I'm coming from the world of gotcloud where when a step in the pipeline finishes a file called all.done gets created for that step. So in the event...
View ArticleWarning messages when perform GenotypeGVCFs
Hi, I am running a variant calling analysis using GATK 4.0.1.2 suite on 25 human subjects. After I use CombineGVCFs to have a single gvcf file and run GenotypeGVCFs, the log repeatedly shows WARN...
View ArticleHaplotyper creating vcf files but stopping before reading SNPs
Please forgive me if this is a naive question because I am new to gatk. I am using HapltoypeCaller to call SNPs using a pseudo reference I have created from my sequence data (no reference available and...
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Is it a bug for the Mutect2
Hi, I am using the Mutect2 (gatk-4.0.2.0) paired samples to call somatic mutation. Here is my command line: java -jar gatk-package-4.0.2.0-local.jar Mutect2 --reference hg19.fa -I...
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GATK4 or 3.8 for a new pipeline ?
Hello, I am currently designing a pipeline for exome sequencing to detect SNPs, CNVs and structural variants for clinical diagnosis of orphan diseases. I already have an "old" pipeline with GATK 3.8,...
View ArticleGTAK DepthOfCoverage binning window
Hi there, I want to run GTAK tool DepthOfCoverage with a window like every 10000 bases for WGS data, how should I set up the parameter? Can I use --nBins? does it mean nBins= whole genome size / 10000?...
View Article[PICARD] CollectInsertSizeMetrics vs CollectAlignmentSummaryMetrics
Hello, I am getting some confusing results and not sure how to explain them. I am interested in the total number of reads from a PE library that actually mapped to our reference so we can take that...
View ArticleFiltering multi-sample VCFs for low DP
Hi Team, I have a multi-sample VCF file produced by UnifiedGenotyper. I now want to filter this file marking those variants with a low depth. However the DP entry in the info field is across all...
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Deep learning in GATK4
By Sam Friedman, deep learning developer in GATK4 Over the past couple of weeks, there's been a lot of chatter online --and in the press!-- about the applicability of deep learning to variant calling....
View ArticleValues for QD annotation not detected for ANY training variant in the input...
Hi, I am running VariantRecalibrator on 2 WGS using the command: gatk VariantRecalibrator \ -R ./hg38/Homo_sapiens_assembly38.fasta \ -V combinedgVCF.g.vcf.gz \ --resource...
View ArticleVQSR / CNN filtering for small (~100) gene panels
Hello, I'm trying to perform germline variant calling on a panel with ~100 genes. I was wondering what the bare minimum (in terms of sample size) would be for variant filtering via VQSR. If the sample...
View ArticleIUPAC nucleotide codes (picard)
I am trying to use picard (tool: FastqToSam) where the non-standard letter 'X' have been introduced (for reasons not relevant for the question) but picard thows an exception - perhaps expected:...
View ArticleGenomicsDBImport problem with versions 0.9.0 and 0.9.2
Hi, I don't know if it's a bug, but whenever I try to do a GenomicsDBImport I get an error, no matter which file I use. The command I run is (using GATK 4.0): gatk GenomicsDBImport -V...
View ArticlePerformance troubleshooting tips for GenotypeGVCFs
Hi, I am running a GATK4 variant calling analysis on few hundred Solanum lycopersicum samples via bcbio (species is diploid, 1gigaBase reference) . Everything went fine up to and including importing to...
View ArticleCombineGVCFs assigns incorrect reference allele in GATK3.7 and GATK4
I'm analyzing 284 exomes using GATK 3.7-0-gcfedb67. My workflow is to run HaplotypeCaller on each individual exome split into 32 bed files. After HaplotypeCaller I combine the 32 split g.vcf files...
View Article(Howto) Run GATK4 in a Docker container
1. Install Docker Follow the relevant link below depending on your computer system; on Mac and Windows, select the "Stable channel" download. Run through the installation instructions and initial setup...
View ArticleCreate a PoN from samples with different technical backgorund?
I read on your somatic mutation variant calling tutorial that even unmatched PoN could help for detecting sequencing artifacts. But the normal samples in my laboratory came from different exome...
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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 and be sure to read about updates also within the Comments section. This exploratory tutorial...
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