Lifting over VCF's from one reference to another
liftOverVCF.pl Contents 1 Introduction 2 Obtaining the Script 3 Example 4 Usage 5 Chain files Introduction This script converts a VCF file from one reference build to another. It runs 3 modules within...
View ArticleIs 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 ArticleBenefits of running UnifiedGenotyper on multiple samples at the same time
The best practice guide states to call variants across all samples simultaneously. Besides the ease of working with one multi-sample VCF, what advantages are there to calling the variants at the same...
View ArticleVariant Quality Score Recalibration (VQSR)
Slides which explain the VQSR methodology as well as the individual component variant annotations can be found here in the GSA Public Drop Box Detailed information about command line options for...
View ArticleHow should I interpret VCF files produced by the GATK?
1. What is VCF? VCF stands for Variant Call Format. It is a standardized text file format for representing SNP, indel, and structural variation calls. See this page for detailed specifications. VCF is...
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 ArticleAdding Genomic Annotations Using SnpEff and VariantAnnotator
Adding Genomic Annotations Using SnpEff and VariantAnnotator IMPORTANT ANNOUNCEMENT: Our testing has shown that not all combinations of snpEff/database versions produce high-quality results. Please see...
View ArticleUsing the GATK API to annotate my VCF
I just quickly wrote a set of Tools to annotate my VCFs ( http://plindenbaum.blogspot.fr/2013/02/4-tools-i-wrote-today-to-annotate-vcf.html ) For example, one of those tools uses a BED/XML file indexed...
View ArticleGATK's quality scores on VCF files
Hi, According to the link http://www.1000genomes.org/wiki/Analysis/Variant Call Format/vcf-variant-call-format-version-41. quality score (phred score) is defined as below. (i.e. 1% error rate is equal...
View ArticleCan SelectVariants be used to limit VCF files by interval list
Hello I would like to subset a VCF file to only save a few specific regions of the whole genome. I know some of your tools allow for an interval list to be used to subset the region analyzed. Do you...
View ArticleDepth Reporting in DP and AD changes when VariantAnnotator run
Hello, I am trying to filter some of my high-coverage samples based on a minimum depth and have found that the value stored in the DP INFO field and the AD genotype tag changes depending on whether or...
View ArticleExtracting de novo mutation from multi sample vcf
Hi all, I'm currently trying to extract de novo mutations from my multi-sample vcf files (trios). I've already read the VCF file specification documentation but wanted to check if I got this right. So...
View ArticleGATK: basic VCF indel output question
Hi, I'm having problems understanding a GATK output VCF. I have read the VCF standard, but I'm obviously missing something. I /think/ I understand how SNPs and short indels are represented, but clearly...
View ArticleVariant Annotator of a multisample vcf, how to set the bam files in the args
Hi, I have a vcf containing multiple samples. I would like to put the bam files also as input for the Variant Annotator but how does the variant annotator know which bam is for wich column in the vcf?...
View Articlewrong QD value in a vcf file
Hello, Here is part of a vcf generated by GATK Unified Genotyper : chr4 106196323 . TCAGA T 32729.73 LowQD...
View ArticleVCF contrasts - workflow
I am just starting with GATK but even though I have looked and looked I can not find a simple walkthrough of having many VCFs and running a range of contrasts based on sample data. I guess this must be...
View ArticleUnifiedGenotyper doesn't generate 1 vcf per sample when bams from multiple...
we are running tests trying to get UG to produce 1 vcf per sample when inputting bams from multiple subjects. our situation is complicated slightly by the fact that each sample has 3 bams. when we...
View ArticleINFO column in Mills dataset
Hi all, I have been looking for a documentation for the INFO column in the VCF of the Mills indels in the GATK resource bundle (Mills_and_1000G_gold_standard.indels.b37.sites.vcf.gz), but to no avail....
View ArticleFalse positives in variant calls?
Hello all, We've just started using GATK in order to perform variant calling in a non-model teleost fish. The fish genome is highly repetitive (>65%), and also suffers from the whole genome...
View ArticleUnifiedGenotyper failure
I have twice run UnifiedGenotyper and the resultant .vcf file contains only part of chromosome 20. I do not see what I am doing wrong. Neither do the other two people in the lab who have extensive...
View Article