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Wrong results with QD,bug?
@valentin @Geraldine_VdAuwera Hello, I do HaplotypeCaller twice，then compared the result vcf files with notepad++ plugin Compare.I found some different value about the QD annotation: java -Xmx12G -jar...
View ArticleSingle-Sample Genotyping: Different Workflow?
Hi, If I need to independently call and genotype a single sample, is there a different workflow or set of GATK tools and settings that I ought to use instead of using haplotypecaller to generate a GVCF...
View ArticleCombineGVCFs includes header from dbsnp file?
Dear GATK team, I have encountered some strange behaviour when running CombineGVCFs (version 3.7-0). When I include a dbsnp file with the -D flag, it appears the entire header of this file is included...
View ArticleGenotypeGVCFs: no records in VCF
Dear GATK team, I am having troubles calling genotypes on *.gvcf produced by HaplotypeCaller in GVCF mode. When I run GenotypeGVCFs (GATK 3.5), I get only header in resulting VCF file, but no records....
View ArticleVariant in VCF of multiple samples called by HaplotypeCaller absent in their...
Hello GATK team, I followed GATK best practices and called variants with haplotypecaller in 6 exome samples. However, in 4 patients (total) I have a variant on Chr12 that is absent in the BAM file. the...
View ArticleProblem with GATK pipeline, merging VCF and ped file.
Hi to all I have just started using GATK and I have few question about some tools and about the general workflow. I have 3 exome-seq data from a trio and I have to detect rare or private variants that...
View ArticlePlease help me to interpret this line. How come I have this disease?
chr1 53676448 . G A 1495.77 PASS...
View Articlehow to download the lasted cosmic vcf file
I want to run Mutect2 with the lasted cosmic file. But I can't find where to download it. I search the Forum, and find others may advise to download cosmic file from...
View ArticleSnpEff html and .vcf file result are not matching
Asslamu Alikum I have successfully managed to run SnpEff for my vcf files. However, the count of missense variants in my html file and the VCF file generated by SnpEff are different. Missense in HTML:...
View ArticleHow does HaplotypeCaller discriminate between heterozygous and homozygous...
Dear members of the GATK team I am using different GATK modules to detect some SNPs in my RNASeq data set. I did a test run for one individual to get an idea about the output of HaplotypeCaller. I know...
View ArticleHaplotype Caller Makes SNPs look like INDELS
I'm using the HaplotypeCaller to look at SNPs related to antimicrobial resistance and am getting a result that looks like this: NC_011035.1 2049708 . CCGGCG C ... NC_011035.1 2049714 . C CAAGAA ... I...
View ArticleVariantsToBinaryPed java.lang.ArrayIndexOutOfBoundsException: -1
Hello, can you please help me sort out the following error in running VariantsToBinaryPed: java -jar /sb/project/fkr-592-aa/data/GalWaRat/bin/third/gatk-3.7/GenomeAnalysisTK.jar -T VariantsToBinaryPed...
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CombineVariants in GATK4
Is it planned to add CombineVariants tool into GATK4.0 toolkit (it existed in previous GATK versions)? The only similar tool currently available in GATK4.0 Beta is GatherVCFs which has very limited...
View ArticlePicard SortVcf changing VCF file version
I am using Picard SortVcf to reorder the order to match the order of my reference genome and BAM files. And it works great, however it seems to be changing the VCF format from 4.0 to 4.2, and this is...
View ArticleWhen I call Indels from my vcf file using GATK analysis tools I ger an Error!
Hi I used the GATK pipeline until I got a vcf that had SNPs and Indels, so I used GATK Analysis tools to remove SNPs and keep Indels. But after adding the reference genome, dictionary and index I get...
View ArticlePicard LiftoverVcf
I am having a problem with picard's LiftoverVcf. I am trying to Liftover hapmap files (downloaded plink files from hapmap and converted to vcf using plink) from ncbi36 to hg38. I was able to do this...
View ArticleThe result of Mutect BAM and vcf is different.
I got some vcf result using mutect. but I have some question about the result. the Allele frequency in vcf is so strange. for example, the below is my result. chr4 1809127 . C T ....
View ArticleProblem with LiftoverVcf
It is my first time running the LiftoverVcf, but I saw that many other users passed through difficulties similar to mine but not exactly the same. I'm trying to convert a vcf file from Hg18 to Hh19....
View ArticleUse vcf from HaplotypeCaller as normal_panel with Mutect2 (GAKT4.beta.6) ?
Hi, I am trying to find somatic mutations in blood samples. The same samples were used previously to detect germline variants with HaplotypeCaller. Does it make sense to use the vcf obtained for a...
View ArticleError in SortVcf
I have been going through this problem. Is this very common and is there any solution to this error. Exception in thread "main" java.lang.IllegalStateException: Key . found in VariantContext field INFO...
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