Clik here to view.
HaplotypeCaller may fail to detect variant with the same reads with a...
I have experienced a variant detection issue with confusion. The png file attached is the result of exact same NextSeq experiment but the read extraction range is different. NextSeq2_point.bam: bam is...
View ArticleRealignerTargetCreator ERROR MESSAGE: Invalid command line: Failed to load...
Hi, What does this error msg try to tell me? Is the 'reference dictionary' the refseq? If yes, why can't it load it (the file is OK, sourced from the bundle, successfully used with bwa and Picard)....
View ArticleMutect2 (GATK4) annotations
Hi, I've encountered some issues when including annotations running Mutect2 in GATK4 (v4.0.1.2). My use-case is an unsupported feature of GATK4 (calling somatic variants without a matched normal...
View ArticleGATK4 CollectHsMetrics - How to avoid the overlap of adjacent intervals ?
Hello, I'm trying to access the quality of my targeted experiment, and I'm interested on saving the per target information using the --PER_TARGET_COVERAGE argument. However, I observed that when...
View ArticleBQSR and False Negatives?
I am looking at GATK Best Practices for Data Processing and Germline Variant calling. I see that the workflow calls for base quality score recalibration using BaseRecalibrator...
View Articlemodifying the processing-for-variant-discovery...inputs.json
Dear GATK Team, I just successfully converted my fastq files to ubam and wanted to do a local data preprocessing using the uBAM to analysis-ready BAM universal pipeline. I realized that I have to call...
View ArticleCan I use GATK workflow for plant (Cannabis) to detect variants?
Can I use GATK workflow for plant (Cannabis) to detect variants?
View ArticleInstalling GATK4 via Conda
Hi there! I have a small problem, or a suggestion for improvement, related to the use of (Mini)conda and GATK4. I'm not entirely sure if this forum is a right place to ask this because I don't really...
View ArticleClik here to view.
Seeing multiple calls for the same position
Hello, I am running a trio through the best practices pipeline for 3.7 and finding an unexpected result. I am seeing some positions that are being called multiple times with different calls. First, as...
View Articlem2 gatk4 oncotated maf output includes rejected mutations
The oncotated maf output includes many rejected mutations (using the configuration from the public spaces). This is bad practice. The unfiltered VCF (or preferably a tsv) should have these sites but we...
View ArticleCan GenotypeGVCFs be ran without filtering?
For bacteria genomes I use the "Best Practices" and the HaplotypeCaller to call variants. I would like to output a VCF containing all positions I can then parse on my own. I'm using -ERC BP_RESOLUTION...
View ArticleCalculateGenotypePosteriors - skip non-diploid sites?
This is more of a feature request than anything else. I'm implementing the genotype refinement best practices guidelines for some trio WGS data sets. The probands are mostly male, and chrY causes...
View ArticleProblem parsing interval list file to GenomicsDBImport
Hello, I'm trying to combine 6 GVCF files into a single VCF file using GenomicsDBImport + GenotypeGVCFs with GATK4. I'm still using GATK4.beta5, since I'm not able to find the link to GATK4.beta6. My...
View ArticleRecommended protocol for bootstrapping HaplotypeCaller and BaseRecalibrator...
I am identifying new sequence variants/genotypes from RNA-Seq data. The species I am working with is not well studied, and there are no available datasets of reliable SNP and INDEL variants. For...
View ArticleTask JointGenotyping.ImportGVCFs failed with message 10: failed to copy files
Task JointGenotyping.ImportGVCFs failed on joint discovery of 34 exome samples: When I look into the stderr.log file: 08:33:54.012 INFO GenomicsDBImport - Starting batch input file preload 08:33:59.013...
View ArticleMeaning of error: expected haplotypes.size() >= eventsAtThisLoc.size() + 1
Hi, I am running HaplotypeCaller (GATK 4.0.0.0) in genoype-given-alleles mode using a VCF of common coding germline variants. Please see the error below. Can anyone help to point me in the right...
View ArticleVariantFiltration and BaseRecalibrator
So I've created a pipeline to make a known.snp.vcf for my species without known snps for BaseRecalibrator: For a subset of my samples (~5% of my dataset, 10 samples): I ran HaplotypeCaller on each bam...
View Articleerror in Mutect2 when using dbsnp?
I am running Mutect2 with various options. Most options are running as expected, but when using the --dbsnp version I am now seeing an error: A USER ERROR has occurred: dbsnp is not a recognized option...
View ArticleSortSam in GATK4.0.1 fails, Picard 2.11 SortSam works on the same file
I try to use the standard workflow sequence with GATK4 as it was published in the tutorials last year for Picard/GATK combination. I called the SortSam tool as follows: ./gatk --java-options "-Xmx4G"...
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...
View Article