GATK 3.8 Dictionary cannot have size zero
Hi, today I wanted to update my pipeline from running on GATK3.6 to 3.8. But now it complains about the dictionary. ERROR -- ERROR stack trace java.lang.IllegalArgumentException: Dictionary cannot have...
View ArticleGATK 3.8 logger ERROR
Hi, after updating to GATK 3.8 I found the following ERROR in my log file. ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:f...
View ArticleSNV gets dbSNP annotation in one sample, doesn't get annotated in another one
Hello everyone, I recently run HaplotypeCaller for GATK3.7 on a series of samples (several GATK runs performed at the same time), using the latest release of dbSNP(150). This was the command line I...
View ArticleCalling copy number from WGS data using PON from different platform
Hi, I'm trying to call somatic copy number form WGS data using the workflow laid out in cnv_somatic_copy_ratio_bam_workflow.wdl However, I do not have a panel of normals for the sample. The data was...
View ArticleFastaAlternateReferenceMaker for polyploid
Are there any tools similar to FastaAlternateReferenceMaker that can create fasta sequences from a pooled-sequencing vcf file? The sample data came from 25 pooled diploid individuals, so I created the...
View ArticleIs GATK overestimating the heterozygous calls?
Hi, I have 24 genotypes distributed in 4 different populations. I used HaplotypeCaller with the option –ERC –GVCF and obtained the vcf file for each genotype. Then combined all the genotypes to a...
View ArticleAnnotation modules in Haplotypecaller and Genotype gVCFs
I am performing WGS using the GATK best practice guidelines for the '-ERC GVCF' cohort analysis workflow. If I ran HaplotypeCaller in default mode (i.e. without specifying any particular annotation...
View ArticleClean version of dbSNP in the GATK resource bundle
Hi I understand that version 129 of dbSNP is considered clean and does not share data from other databases such as 1000G projects. What steps of the variant calling in WGS/WES analysis can be affected...
View Articlecan I use indel realignment bam file for extract SNPs?
Hi everybody, I'm following the pipeline for VC in RNAseq and I have some doubts. At that moment I've done: 1)Split'N'Trim and reassign mapping qualities (output: split.bam) 2)Indel Realignment: at...
View ArticleVariantRecalibrator for bacterial genome annotation
Hello!, i want to filter bad variants using VariantRecalibrator, the problem is am a bit lost which are the databases i can use as resource and should i have them on my local machine? My input file is...
View ArticleLocation of documentation for option types
Hi, Could you provide a pointer to the place in the documentation where types such as RodBinding[VariantContext] ArrayList[String] List[Type] Set[File] etc and their exact usage are described? Despite...
View ArticleClock drift error
I'm trying to use genotypeGCFs on 350 small gVCF files (from bacterial genomes) and I'm getting this "clock drift" error: INFO 13:02:46,006 ProgressMeter - chr1:44001 0.0 3.0 h 15250.3 w 2.0% 6.3 d 6.2...
View ArticleMissing version label for the downloaded GATK release...
Hello, I am currently developing a pipeline for genome assembly and annotation, in which GATK is one of many dependencies. Since the current version of GATK (3.7) still need manual registration and...
View ArticleIllegalArgumentException: samples cannot be empty
I am trying to run HaplotypeCaller on some data that I know is messy and would fail some of the filters, so I have run it both with and without --disableToolDefaultReadFilters. Either way I don't get...
View ArticleTruth or control samples - Variant calling
Are we able to incorporate truth/control samples in addition to dbSNP when calling variants with GVCF (cohorts) or the traditional way with HaplotypeCaller. There are for example situations where the...
View ArticleMuTect2 beta --germline_resource for build b37
Hi - I'm looking to run MuTect2 beta using the --germline_resource option. However, I've consistently used the b37 genome build throughout my analaysis, while the suggested resource (gnomad) appears to...
View ArticleBase Recalibration
Hi I am not much familiar with bioinformatics and SNP Genotyping. As I am trying to identify the SNP in my sample from SRA Database so this the pipeline i am following I - STAR Aligner to mapping II -...
View ArticleGATK workshop (Oxford)
Hi! GATK team, I remember there is a workshop in Oxford (9/18~9/20). Is it cancelled? Thanks! Dada
View ArticleTool documentation
Where has the tool documentation gone to? I keep getting 404 errors when trying to follow links to specific tools (from google) or the general tool documentation area.
View ArticleRegarding Gatk output
Hello, I want to identify snps in my sequencing data.I am new in this field so i am just following guideline that you provided. i have paired end sequencing data (one sample) and according to...
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