Does BaseRecalibrator require a vcf file ?
Hello I am following the gatk best practices guide, and using the 2 stages BaseRecalibrator process. The first recalibration is going well, the second one, produces an error like described below, I...
View ArticleThe provided VCF file is malformed at approximately line number 37:...
Hi! I try run GATK with SelectVariants. But the error message was generated. ERROR MESSAGE: The provided VCF file is malformed at approximately line number 37: unparsable vcf record with allele X My...
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 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 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 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 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 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 ArticleMutect VCF output
Hi, Can someone please explain to me what 50 columns represents individually in variant output file of MuTect: chr1 49530 TCGxTTG C T cancer nromal 0 NOVEL COVERED 0.997898 0.997898 1 1 1 145 1...
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 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 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 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 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 ArticleClik here to view.
Missing reference allele in GVCF file after running HaplotypeCaller
Hi, I used HaplotypeCaller in GVCF mode to generate a single sample GVCF, but when I checked my vcf file I see that the reference allele is not showing up: 22 1 . N <NON_REF> . . END=16050022...
View ArticleWhat exactly does the --minReadsPerAlignmentStart flag specify in...
Specifically, what does the 'start' component of this flag mean? Do the reads all have to start in exactly the same location? Alternatively, does the flag specify the total number of reads that must...
View Article