How To Load A Custom Genome With The Readvcf() Command (Bioconductor)

Hello,

Loosely imitating http://www.bioconductor.org/help/workflows/variants/

library(VariantAnnotation)
readVcf("myvcf.gz")

This fails - readVcf requires "genome" argument... which I do not have because I work with a nonmodel organism. So how can I create a custom genome object that makes it possible to load a VCF from a non-model organism into R?

I want to have my Vcf in GRanges format for subsequent plotting with ggbio....

Thanks & kind regards, Yannick

vcf r

• 3,461 views • link

written 13.9 years ago by Yannick Wurm

1 answer

Whoops! It turns out that the custom genome doesn't really have to be a genome - any character string will work! Thanks Bioconductor mailing list for the answer

  readVcf("myvcf.gz", "myDogRex")    # no problem!

• 0 views • link

written 13.9 years ago by Yannick Wurm

More posts like this

Add GenomicRanges to SummarizedExperiment
written 9.6 years ago by s.w.vanderlaan •

Hi, I've got RNAseq data which was processed and given to me in a text-file. The rows are EnsemblIDs, and the columns the individuals with …
What is an optimal normalization approach for comparing GTEx RNASeq normal vs TCGA tumor samples?
written 10.9 years ago by Samir

I am trying to compare RNA-seq read counts from normal tissue samples from GTEx to tissue-level matched TCGA tumor samples. Since TCGA has also a …
VariantAnnotation parallel usage
written 11.7 years ago by russhh

Hi, I'm trying to run a bioconductor variant annotation workflow, similar to that described [here][1] but I'm having trouble running my code in parallel over …
Synteny Diagram In Biopython
written 12.4 years ago by Pappu

I am trying to compare the synteny of a homologous gene of a set of embl files. I wrote the following script in Biopython which …
Visualize Vcf In Igv
written 12.4 years ago by mad.cichlids

when i was trying to use R to visualize my VCF file I first loaded the file and compressed it: <pre><code> vcf <- readVcf(str.vcf, "Genome") …
Snp Calling Error By Gatk Unifiedgenotyper Program
written 12.8 years ago by Tonyzeng •

HI, I have tried to do SNP calling using the GATK UnifiedGenotyper program,here is the command, (mouse) <pre><code>java -jar /raid1/rzeng/softwares/GenomeAnalysisTK-2.7-4-g6f46d11/GenomeAnalysisTK.jar -glm BOTH -R genome.fa -T …
Why Does Vcftools Vcf-Annotate Produce An Empty File
written 13.4 years ago by ttom

I am trying to annotate a VCF file by adding DBSNP information to the INFO column, using the given below annotation file <pre><code>CHROM FROM INFO/DBSNP …
How To Convert A Genome Mappability Data (Gem-Mappability) To Ucsc Compatible Format?
written 13.8 years ago by Bojan •

I am trying to calculate genome mappability of some yeast species using GEM-mappability (<a href='http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030377'>http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377</a>) which was used for the calculation of the USCS Genome …
Tool: Variantannotation Package (Bioconductor)
written 14.0 years ago by Malachi Griffith

Using the Bioconductor [VariantAnnotation][1] Package to [Annotate Genetic Variants][2] > The VariantAnnotation package has facilities for reading in all or portions of Variant Call Format …
Getting A Table Of Genotypes (Snps) Into A Genome Browser
written 14.9 years ago by Yannick Wurm

I work with a non-model organism which is absent from online genome browsers. I have genotypes at 5000 loci for 100 haploid individuals. This is …