Is there any description or a marker of Indels in VCF file?
Hello, I'm maybe missing something obvious but it seems a GATK vcf file does not tell a given variant is SNP, Insertion or deletion. Did I missed some command when I called variations? I can easily...
View ArticleInterpreting '.' in AD field of
Hi, I'm doing a variant analysis of genomic DNA from 2 related samples. I followed the up-to-date Best practices using HaplotypeCaller in GVCF mode for both samples followed by GenotypeGVCF to compute...
View ArticleI/O error loading or writing tribble index file for VCF file
I am performing analysis on mm9 (mouse). Downloaded VCF file from UCSC. Removed chr*_random and chrM Used vcftool v4.0 prepared two files ONLY INDEL and ONLY SNPS vcf files (DBINDEL, DBSNP) Please...
View Articleseen variant in a genome browser doesn't appear in vcf file, using...
Hi GATK team, I ran HaplotypeCaller on a bam file that I pre-pprocessed according to your Best-Practices. When looking in a genome browser at this bam, I encountered a position that seems to have a...
View ArticleA single pass mechanism to add multiple annotations to vcf
Hi, I was wondering if there is a nice way to apply multiple processing steps to each variant (or a group of variants) as they are read so that the variant file is not read again and again. My...
View ArticleERROR MESSAGE: Your input file has a malformed header
Dear GATK team, I have got an error message while using RealignTargetCreator -- ERROR MESSAGE: Your input file has a malformed header: there are not enough columns present in the header line: #CHROM...
View ArticleAD field has too many values for Biallelic site:
Hi I've just noticed this in some records, in some bi-allelic sites the AD field for some samples can have far more than 2 columns and the values can be separated oddly. For example in the record at...
View ArticleProblem to merge vcf files
Dear team, I am new to GATK and I am having a hard time simply trying to merge vcf files. I have tried to solve the problem by referring to the guide and to previous posts, but nothing woked. Actually...
View ArticleQUAL score for monomorphic positions in VCF files
I used the EMIT_ALL_SITES option with Unified Genotyper. For polymorphic sites, the quality score (QUAL field) corresponds to the Phred scaled probability that a REF/ALT polymorphism exists at this...
View ArticleVarian quality recalibration annotations.
Hello, What annotations are recommended to be used for the variant recalibrator for an exome sequencing project? I am using the Ion proton system so my VCF files are automatically generated after the...
View ArticleMerging batched call sets - RETIRED
This procedure is deprecated since it is no longer necessary and goes against our Best Practices recommendations. For calling variants on multiple samples, use the Best Practices workflow for...
View ArticleCombineVariants for different samples
Hello everyone, I have used the ion proton system to sequence 15 sample exomes so far. In this system, only 3 samples can be run at a given time, so I essentially have five sets of samples. Is it still...
View ArticleResults for genotype concordance
Hello, I just ran genotype concordance in order to determine how similar two samples were. However, in the output, everything is showing up as zero, the NRD determined is 1 and the overall genotype...
View ArticleDiagnoseTargets output -reference allele?
I have used a VCF file that was produced by GATK for the -L option of DiagnoseTargets, but I get the alternative allele from the original VCF as the reference allele on the output vcf from Diagnose...
View ArticleTriallelic sites in MuTect
Hello, I am running MuTect 1.1.7 on some amplicon data that targeted several specific genes. There's one documented mutation in particular that MuTect correctly identifies, but rejects due to,...
View ArticleVCF files for Indels and SNPs
Hi, I am following the Best Practices for DNAseq analysis and have 2 quick questions: 1. I wanted to confirm if the VCF files produced after the VariantRecalibrator and ApplyRecalibration steps for SNP...
View ArticleUsing Variant Filtration - RETIRED
This tool is not deprecated, but this article is now superseded by the method article on JEXL expressions. VariantFiltration For a complete, detailed argument reference, refer to the GATK document page...
View ArticleHaplotypeCaller SB field for multiple-alts
The SB field of HaplotypeCaller output is not described terribly well as far as I can find. ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the...
View ArticleGenotype based on PL is not consistent with AD values
Hi, We found this line in a VCF file and we're confused why GATK gave 1/1 when Ref has greater reads than Alt chr10 5129483 . A C 49.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=-2.152;DP=29; GT:AD:DP:GQ:PL...
View Articlehow to split multiple samples in a single VCF file?
I finally got the filtered VCF file from PWA + PiCard + GATK pipeline, and have 11 exome-seq data files which were processed as a list of input to GATK. In the process of getting VCF, I did not see an...
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