Interface with BEAGLE Software - RETIRED
Note: As of version 4, BEAGLE reads and outputs VCF files directly, and can handle multiallelic sites. We have not yet evaluated what this means for the GATK-BEAGLE interface but we believe it renders...
View ArticleignoreFilter in VariantRecalibrator
Hello dear GATK Team, it seams that the ignoreFilter Argument in VariantRecalibrator does not work. I want to include variants with LowQual filter in the calculation, but cant find the right way to do...
View ArticleAdding priors to UnifiedGenotyper.
I don't know if this question has been asked, if so sorry. When using UnifiedGenotyper, I was wondering if it was possible (via hidden command option, etc) to use a VCF file as a prior. Currently I...
View ArticleQuestions about my VCF file generated by UnifiedGenotyper and cannot do the...
Hi, I known that this question should not post to the GATK forum because the ERROR told me that "Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself."...
View ArticleReading Vcf Files from Strelka
Strelka produces vcf files that GATK has issues with. The files pass vcftools validation, which according to the docs is the official validation, they do not pass ValidateVariants. VariantEval can't...
View ArticleVCF Liftover header stringency
I am trying to liftover from NIST b37 to hg19. I have all the files I need and I can kick off the liftover just fine, but I keep running into problems because the NIST vcf has tags in the variant line...
View ArticleUnified Genotyper: VCF files where genotype is not called
Hi. I have run UnifiedGenotyper and the output VCF file has : When the genotype is called you get: GT:AD:DP:GQ:PL 1/1:0,1:1:3:37,3,0 (i.e. five colon-separated fields as expected) When the genotype is...
View ArticleRank Sum Tests
Hey guys, im struggeling with some statistics given by the vcf file: the Ranksumtests. I started googleing arround, but that turned out to be not helpfult for understanding it (in may case). I really...
View ArticleAppending QUAL scores from multiple vcf files into a single vcf output
Hi, I have a vcf files of interest, and would like to append QUAL scores ONLY from CORRESPONDING genotypes in OTHER vcf files, all into a single vcf output, so that the corresponding QUAL scores will...
View ArticleReg. Adding header line to Ensembl vcf file
Hello I am working with canine genomes and donwloaded the reference file (ftp://ftp.ensembl.org/pub/release-73/fasta/canis_familiaris/dna/Canis_familiaris.CanFam3.1.73.dna.toplevel.fa.gz) and variation...
View ArticleFILTER values and other VCF file attributes after ApplyRecalibration
So I have used the latest GATK best practices pipeline for variant detection on non-human organisms, but now I am trying to do it for human data. I downloaded the Broad bundle and I was able to run all...
View ArticleFiltering Variants using the Format Column + JEXL Oddities
Hi Team, I have a VCF which I'd like to filter by variant frequency. The problem is, my frequencies are percentages rather than decimals. Is there a workaround in JEXL which allows it to parse the '%'...
View ArticleWhen my reads quality and alignment is good, why the VCF files contains ./....
My exome-seq reads quality is pretty good (120M reads) and the alignment using bwa is more than 95%. I use GATK to do the variant calling, however, the vcf output from VQSR contains many './.' fields,...
View Articlecombine snp and indel vcf
is there any way to combine a snp vcf and indel vcf (generated with the UnifiedGenotyper) later? in the way that there is only one row per locus? regardless how I combine (I tried mainly...
View ArticleUse VariantFiltration/SelectVariants tool to choose SNPs matching a position
Hi, I was wondering if you could use the toolkit to generate a separate VCF file containing only SNPs that are found at a predetermined chromosome and base pair position. I have a plink file which I...
View Articlewhat interval files do you guys use for human exome variant calling?
I downloaded my intervals files from UCSC human exome captured file (hg19_exome_sorted.bed), but I keep getting lots of "./." in the final VCF files. I asked before in this forum, and I remember...
View ArticleOne called and one missing allele in vcf file
How can an individual in a vcf file have one called and one missing allele? I generated a dataset in GATK and did not encounter this in my GATK generated vcfs. However in comparative data vcfs I saw...
View ArticleQuestion about criteria selecting variants
As I said in my last post about splitting my 11 samples from the recalibrated VCF file. I now have a different question which is how to set up a criteria to select variants from this 11-sample-combined...
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 Articlehow to understand this "1/1:0,1:1:3:36,3,0" in VCF?
One of my samples has this entry "1/1:0,1:1:3:36,3,0" in the information field, and from my understanding, the genotype is homo variant, because it has 1/1. However, I do not understand why. Since it...
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