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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...

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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...

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Benefits 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...

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Variant 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...

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How 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...

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Problem 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...

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Adding 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...

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Using 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...

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GATK'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...

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Can 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...

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Depth 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...

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Extracting 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...

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GATK: 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...

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Variant 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?...

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wrong 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...

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VCF 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...

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UnifiedGenotyper 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...

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INFO 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....

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False 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...

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UnifiedGenotyper 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...

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