Germline CNV Tutorial available?
Is there a tutorial available for calling CNVs in germline DNA with GATK4? I see an earlier post for somatic CNVs but could not locate one for germline CNVs.
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Using GATK: create a F0 SNP library and then genotype F2 sample using it
Hello GATK community, I would like your comments/suggestions for my strategy. I have F0 samples with two different phenotype. I have F2 samples with unknown phenotype. I would like to create a library...
View ArticleHaplotypeCaller is extremely slow
Hi Everyone, This is the first time I run GATK and do variant calling. I have been looking around the internet for a while, but haven't been able to resolve my issue. I run the following command to do...
View ArticleHaplotypeCaller warnings DepthPerSampleHC
Hi I'm trying to do a multisample variant call using several bam files in the following cmd /mnt/fastdata/md1jale/software/gatk-4.0.1.0/gatk HaplotypeCaller -R /mnt/fastdata/md1jale/reference/hs37d5.fa...
View Articlehow to let GATK support Coordinate Sorted Index (CSI) format of bam file
Since samtools 1.0, csi indexing format of bam file is specifically used for any other organisms with long chromosomes ( > 536Mb). Could you help me figure out how to let GATK SplitNCigarReads...
View Articleno. of cores utilization in haplotypcaller in GVCF mode
Hi, I am running Haplotypecaller (v4.0.1.2) (not the spark version) on some WGS samples on a SGE (Sun grid Engine) cluster. When I am submitting a job to my cluster, I am asking for 1 core (on an 8...
View ArticleCollectRnaSeqMetrics - no coding reads found
Hello, This is my code: java -jar picard-2.8.0.jar CollectRnaSeqMetrics \ I= bam/Aligned.sortedByCoord.out.bam \ O= output.RNA_Metrics \ REF_FLAT= bam/refFlat.txt \ STRAND=NONE \ RIBOSOMAL_INTERVALS=...
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Variant Quality Score Recalibration (VQSR)
This document describes what Variant Quality Score Recalibration (VQSR) is designed to do, and outlines how it works under the hood. The first section is a high-level overview aimed at non-specialists....
View Article[GATK4 beta] no filter-passing variants in Mutect2 tumor-only runs using...
Hello, I would like to ask your advice on the tumor only mode of Mutect. I ran GATK4 beta.3's Mutect on 20 tumor samples using tumor-only mode, and found no variant passing filters. Every variant is...
View ArticleReCapSeg Overview
Introduction ReCapSeg is a copy-number variant detector that runs on user-defined target regions, which can correspond to exomes, gene panels, or arbitrary windows. ReCapSeg uses a Panel of Normal...
View ArticleBatch options in GenomicsDBImport
Hi, We are planning to test around 5000 WGS samples for Joint Variant calling and would like to follow as mentioned here https://software.broadinstitute.org/gatk/documentation/article?id=10061 One of...
View Articlegatk4 error: java.lang.IllegalStateException: The covariates table is missing...
Hi, Trying to run GATK4 best practice on AWS batch setup with docker (using SSDs). In most of the time "ApplyBQSR" fails with the following error. Oops... Pipeline execution stopped with the following...
View ArticleError : Duplicate allele added to VariantContext
Hello, I download GnomAD vcf files in GRCh38 (hg19 remap). I want to convert this vcf in a table so i try to use VariantsToTable. But i have this error : The provided VCF file is malformed at...
View ArticleWeb-based Oncotator server
There is a web-based version of Oncotator which you can use for annotation without running anything on your own machine. However, please note that the web-based version is an older version, with fewer...
View ArticleCurrent status of GATK4 GermlineCNVCaller tools and best practices.
Hi, I would like to try out GATK4 for discovering or genotyping germline CNV's in a cohort of few hundred whole genome sequenced samples. I work with non-human species data, but the genome sizes are...
View ArticleRealignerTargetCreater: A USER ERROR has occurred: '-T' is not a valid command.
Hi, I was running GATK RealignerTargetCreater . I ran the same command before with another bam file and it ran fine. Both of the bam files were produced using BWA MEM, sorted, indexed, fixed mate...
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Haplotypecaller calls variants at a deletion region
Hi, I'm having a confusing problem when using haplotypecaller. Basically, I'm using haplotypecaller calling variants among more than 400 M. tuberculosis samples, sequenced with Hiseq2500 platform. I...
View ArticleError running GenomeSTRiP --RCCache: index file is truncated: for...
When running gs_preprocess.sh, I am getting the error "index file is truncatated" on a number of files. Any suggestions for dealing with this? Is there a command to reindex the file? ERROR 13:50:58,287...
View ArticleSampleList annotation returns only one sample while being used in a variant...
Hi there, I have used HaplotypeCaller from GATK4 to call variants on two affected siblings. I put SampleList annotation in the command but only one sample is seen in all of the variants in the...
View ArticleCan't post a discussion on the forum
I've beed trying to post a question and it gets rejected every time. There is nothing special with this question except for the fact that I have a couple of link. When I click on the post discussion...
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