[WDL][Cromwell[ Mounting a directory to the docker for access.
Hi, I am attempting to run Gemini within a docker through WDL and Cromwell. I have installed gemini with no data as the data is too large to be put into a Docker (plus it's bad practice). So I need to...
View ArticleGenomeAnalysisTK Mutect2 Error...
Dear All, I used samtools-0.1.19 got the alignment bam file and index, then I am going to use GenomeAnalysisTK/3.5/java.1.7.0_67 to call variations, but it is not working. If someone can give any...
View Article[GATK 4.0.1.2] unsorted bam in mutect pipeline running in tumor-only mode...
Hello, I need your help on using Mutect2. I tried to call somatic mutations using mutect2_multi_sample.wdl in tumor-only mode with make_bamout = true and scatter_count = 50. It was failed for a small...
View Article[GATK 4.0.1.2] Oncotator fails in CNVSomaticPairWorkflow
Hello, I would like to report an Oncotator failure. Oncotator was run as a part of CNVSomaticPairWorkflow on Google Cloud and oncotator_docker is configured as...
View ArticleInvalid intervals error
Hi, I'm currently working with Genomestrip (version 3.7.GS-r1748-0-g74bfe0b) to do some structural variant calling on some BAMs that were aligned to hg38. Naturally, I used the resources available from...
View ArticleCombineGVCFs looses Genotypes
Hi, I want to merge the g.vcf files I get from HaplotypeCaller using CombineGVCFs. When I do that, the called genotypes vanish. The g.vcf of one sample before merging: NC_000001 13273 . G...
View ArticleGenotype likelihoods from HapMap SNPs
Hello the team, My ultimate objective is to generate genotype likelihoods for SNPs throughout samples. I first used GATK to make a complete VCF file based the SNP variants in HapMap format, and then am...
View ArticleGATK4 Mutect2 bundle resources
Is it possible to get a description of how the gnomAD files (for Mutect2 and CalculateContamination) were generated? Additionally is possible to get some guideline on how they should be generated for...
View ArticleQuestions regarding adding @RG information in Illumina CASAVA Mapped BAM
Dear GATK Team, We received Whole Genome Sequencing data from Illumina and it was mapped by CASAVA. The problem is the BAM files we have do not have @RG tag. But we do have the read group information...
View ArticleHaplotypeCaller on sliced BAMs
Hello I'm trying to do germline calling using HaplotypeCaller. However, I'm only interested in obtaining germline variants for a subset of the genome. To save space and compute resources, I was hoping...
View ArticleGATK sample genotype AD for alternative alleles
Hi all, I have a question regarding the interpretation of AD for alternative alleles. I called variants and subsequently performed joined genotyping, leaving me with a vcf file. Before further...
View Article'Unable to access jarfile MuTect2' Could you explain me where's the problem?
Hello, I'd like to detect somatic mutations using Gatk Mutect2, I have nice Illumina WES experiment. Then publish my results with gatk tool citation of course. Unfortunately a problem has occurred in...
View ArticleGenotypeGVCFs resource problems
Hello, I am using GATK 4.0 to run GenotypeGVCFs on a cohort of 50 samples. After a number of runs which alternately overran assigned cpus or memory (up to ncpus=20, --java-options "-Xmx10g" ), a system...
View ArticleHow can I annotate specific alleles with dbSNP frequencies?
Dear all I would like to annotate a VCF file using dbSNP as a resource VCF, specifically I want to add the 1000 genomes frequency of the called alleles. I tried the VariantAnnotator tool using the...
View ArticleHow many gvcfs can I combine using genomicDBimport (GATK4)?
Hello, I am about to start combining low x gvcfs for many individuals (>4K). In the previous pipeline I had the individuals split into cohorts of ~200 and then hierarchically combined within and...
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Standard practice for VCF filtering for the purpose of fingerprinting via...
Hi all, I was wondering whether I could get some insight into what the standard procedure for `fingerprinting' by prop. IBS for sequencing data is. To be more precise: the proportion IBS between the...
View Articlehaplotypecaller output no AF
Dear GATK team, We are running GATK 3.5 with haplotypecaller and UnifiedGenotyper to consistent with our previous samples: Command: GenomeAnalysisTK.jar -T HaplotypeCaller -R $ref -S LENIENT -I...
View ArticleSNP calling on inverted repeats
Dear GATK team, I have encountered a problem when I used the HaploTypeCaller for variant detection on about 100 plastid genomes. The plastid genome is haploid and contains two large inverted repeats...
View ArticleHow to left normalize multiallelic indels in ploidy=6 vcf files?
Hi, I have generated 26 GVCFs (with ploidy parameter=6), then run GATK-GenotypeGVCFs, successfully obtaining my genotype calls. Now I am trying to left normalize indels, using...
View ArticleHow active regions are identified
Dear GATK team, I am looking into the code of GATK 4.0 and trying to understand how active regions work and are used. Are active regions only those containing substitutions and/or indels? If a region...
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