Making nice plots based on the different metrics from VCF file
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4.0 years ago
Denis ▴ 260

Hi all, I have a multi sample VCF file and i'd like to make a numerous plots with different metrics of the mentioned file for some report/presentation. I use bcftools for that, but wondering if there are any other useful tools or R functions, etc. for my purposes? Thanks!

snp R genome • 4.7k views
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3.1 years ago
pwwang ▴ 40

Try this out: https://github.com/pwwang/vcfstats

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It looks promising. Defenitely worth to try.

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Thanks, let me know if you have any questions in using it.

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4.0 years ago

I wrote http://lindenb.github.io/jvarkit/VcfStatsJfx.html

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3.1 years ago
gb ★ 2.1k

Another option: https://vcf.iobio.io

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5 days ago
cocchi.e89 ▴ 210

Take a look at this: plot-VCF

It allows you to plot different VCF localization and gene analysis straight from your VCF file

As example, you can directly plot the mutation rate (overall, grouped and single-sample) for each gene: plotVCF() gene mutation rate

Or plot variants based on any of their flags in VCF (e.g. Variant Allele Frequency): VCF AF plot

And many more options (well documented on the GitHub page)

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