How to do the annotation on unifiedgenotyper?
I used unifiedgenotyper for the variant calling. Here is the result file that I got: chr1 16919661 . G A 59.74 ....
View ArticleRunning /scripts/genotype+sites.sh example/1000G_MERGED_DEL_2_99615.vcf rundir
An error occurred that I do not understand. `INFO 15:13:07,421 QScriptManager - Compiling 2 QScripts INFO 15:13:10,852 QScriptManager - Compilation complete ERROR -- ERROR stack trace...
View ArticleIndelRealigner has memory issue with longer reads (150bp) and bigger data size
Dear GATK team, Recently, I have got data with whole exon sequence data with longer read length (150bp now VS 75bp before) and bigger data size (4 to 6 GB fastq file for paired end reads together VS 2...
View ArticleGATK 3.8-0 PrintReads fatal error
Hello, Could you please help me to figure out this fatal error in running PrintReads? After I updated GATK to version 3.8-0. I kept getting this fatal error in running PrintReads. I can skip this step...
View Articleit seems that since GATK3.7, info fields from parent VCFs are not kept the...
Hello there, I used to run the following command, to merge VCF from 2 callers (freebayes et GATK); infos fields were first preceded by a unique tag, both in the headers and in each record, to be sure...
View ArticleGATK 3.7 error message: not a strict subset of per read allele map alleles
I am trying to run GATK 3.7 for variant calling and I keep getting this error. Any comments about what this error is? Thanks! ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67): ERROR...
View ArticleCRAM support in GATK 3.7 is broken
I have not been able to get GATK 3.7 HaplotypeCaller to work with CRAM files at all (it has a 100% failure rate so far with our whole genome CRAMs). Based on my analysis of the problem, I don't think...
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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...
View Articleneed GenePattern modules for the latest Picard tools
(repost of part of a mail to Picard team) Is there someone out there having new GP modules for as many as possible Picard.jar subcommands (I love them all) I am preparing a variant training for the...
View ArticleApplyRecalibration error: Unable to create iterator for rod named input
Dear GATK Team, I'm trying to perform variant calling on targeted sequencing data for a cohort of 24 patients. I am following the pipeline described in Best Practices. I have generated individual g.vcf...
View ArticleVariantRecalibrator error
Dear GATK Team, I'm trying to perform variant recalibration on 3 WGS sequencing data. I am following the pipeline described in Best Practices. I have generated individual g.vcf files for each patient...
View ArticleMulti threading in GATK 4 is done with spark now?
In GATK4 noticed I can't use -nt or -nct with tools that support it in GATK 3.x, and I understand that you removed it due to the complexities that it introduced to the code from this discussion:...
View ArticleFILTER column in vcf file from HaplotypeCaller
I used a cohort in running HaplotypeCaller. Some of values in the FILTER column of the resulting vcf file are ".", what does that mean? Here is one example (not all columns included): #CHROM POS ID REF...
View ArticleGenotypeGVCF on pooled data running out of memory despite providing 512GB to...
Dear GATK staff, I am doing SNP calling with GATK 3.8 on whole genome sequences of 12 pools (50 diploid individuals in each pool, genome size ~900 Mbp) of a non-model organism with scaffolded reference...
View ArticleWhat is exact meaning of filtering in vcf
Hi, I have question about output vcf using mutect2. I run the mutect2 using only tumor set, I got this filtering result like this, _**clustered_events;homologous_mapping_event;panel_of_normals...
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variant calling in polyN region using HaplotypeCaller
Hi all, I am using GATK HaplotypeCaller to call the variant, which lies in polyN complex region. java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R...
View ArticleERROR MESSAGE: java.lang.Integer cannot be cast to java.lang.Double
Hi, after running 5 exomes with GATK-v3.3 and HaplotypeCaller, I encountered a very low titv ration in my samples (~2.1) as VaraintEval report indicated. I tried running varaint filtration in these...
View ArticleRealignerTargetCreator -L parameter error
Hi I am using the RealignerTargetCreator tool with the -L parameter on whole genome seq. I have about 670000 regions in my BED file and I am getting the following error: ##### ERROR -- ##### ERROR...
View ArticleVQSR failed with "No data found" with Haloplex panel variant calls.
Hi, Would you please teach me about behavior of GATK 3.8? I ran VariantRecalibrator with GRCh37d5 reference and failed with "No data found". I have three data and two of them are finished successfully...
View ArticleComparison of pairs of tumor samples
Dear GATK, I would like to analyse data from pairs of samples. Each pair is a sample from a tumor and from a cell line derived from that tumor. We expect the tumor samples to be quite heterogenous, and...
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