Question

Making nice plots based on the different metrics from VCF file

2

Entering edit mode

6.0 years ago

Denis ▴ 310

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 • 8.2k views

ADD COMMENT • link updated 2.1 years ago by cocchi.e89 ▴ 290 • written 6.0 years ago by Denis ▴ 310

score 3 · Answer 1 · 2019-10-21

3

Entering edit mode

5.2 years ago

pwwang ▴ 40

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

ADD COMMENT • link 5.2 years ago by pwwang ▴ 40

1

Entering edit mode

It looks promising. Defenitely worth to try.

ADD REPLY • link 5.2 years ago by Denis ▴ 310

1

Entering edit mode

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

ADD REPLY • link 5.1 years ago by pwwang ▴ 40

score 2 · Answer 2 · 2018-12-05

2

Entering edit mode

6.0 years ago

Pierre Lindenbaum 164k

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

quickly wrote a java FX app displaying basic VCF stats : https://t.co/CxURRnKMre pic.twitter.com/chmS9ciuv9
— Pierre Lindenbaum (@yokofakun) April 9, 2018

ADD COMMENT • link 6.0 years ago by Pierre Lindenbaum 164k

score 1 · Answer 3 · 2019-10-22

1

Entering edit mode

5.2 years ago

gb ★ 2.2k

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

ADD COMMENT • link 5.2 years ago by gb ★ 2.2k

score 1 · Answer 4 · 2022-11-24

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)