Vcf Visualization Tool?

Is there any tool that is able to display VCF files on a genome graph or something similar?

vcf visualization genomics

• 705 views • link

updated 15.5 years ago by Pierre Lindenbaum

• written 16.0 years ago by Paulo Nuin

Is there an RFC for VCF or does it just emerge?

• 0 views • link

written 16.0 years ago by Casbon •

1 answer

I think IGV reads VCF.

IGV

• 2 views • link

updated 7.9 years ago by Ram

• written 16.0 years ago by Pierre Lindenbaum

I can't get it to do anything with vcf 3.3 or 4.0. It just complains 'is the file extension correct?. I have '.vcf' files.

• 0 views • link

written 16.0 years ago by Casbon •

You need to index the .vcf file with eg. IGVtools -- vcf4.0 is not supported in this week's release but they say it'll be in there from next week onwards...

• 0 views • link

written 16.0 years ago by Allpowerde

More posts like this

Can vg/minigraph-cactus export a GATK-style all-sites gVCF from a pangenome graph?
written 2 months ago by RianeZ •

Hi, Can `vg deconstruct` or any other vg/minigraph-cactus tool export a GATK-style all-sites gVCF from a pangenome graph? I understand that `vg deconstruct` creates VCF …
What is a rational way to filter VCF and other genome files using BED file with selected genes?
written 9.3 years ago by matveyspr •

What is a rational way to filter VCF and other genome files using BED file with selected genes? I found similar there -- https://www.biostars.org/p/46331/. Is …
Create BED file with restriction enzyme (HindIII) cutting sites of whole chromosome/genome
written 9.6 years ago by peer_wuensche •

Hi there, I would like to display HindIII cutting sites in a genome browser. Ideal would be a bed file or something similar, which enables …
Does vcftools or GATK have an option to skip indels when making alternate sequence?
written 10.0 years ago by severalorks

In my previous question, I asked: I would like to take a vcf file and a reference genome from the 1000Genomes project, and obtain a …
Existing Tools For Viewing A De Bruijn Graph From Raw Reads
written 10.8 years ago by kshitijtayal •

I understand that there are plethora of tools available where you enter the read file and the software will internally build the De bruijn graph …
Graphic tools to depict genes along a chromosome
written 11.5 years ago by hpapoli

Hello, For the presentation, I would like to be able to show the distribution of genes along a chromosome, that is instead of a normal …
Visualizing Maf Of Variants From Vcf Over A Gene Structure
written 13.3 years ago by Khader Shameer

This is a long shot, Given genomic position, allelic information and chromosome info is there any visualization tool out there to plot MAF over …
Motif/Pattern Discovery In Sequencing Data
written 13.8 years ago by Abhi

Hi Guys Just wondering if there is a tool out there that is able to de-novo pattern discovery given the NGS reads as input (mainly …
How To Plot This Kind Of Ma-Plot?
written 14.8 years ago by Zhu •

<img src='http://seqanswers.com/forums/attachment.php?attachmentid=998&d=1317561361' alt='alt text' /> Hi, there. i need helps on plot such kind of graph now. the graph i linked here is from a …
Chromosomal Gene Density Calculation And Visualization
written 15.9 years ago by Paulo Nuin

I am looking for a tool/package/script that would be able to calculate chromosomal region gene density and maybe visualize it. TIA